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Latest articles on Coronavirus - Ahead of Print.
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Table of Contents
February 2019
Volume 149 | Issue 2
Page Nos. 83-306
Online since Monday, June 3, 2019
Accessed 87,861 times.
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EDITORIAL
Creating political commitment for antimicrobial resistance in developing countries
p. 83
Rajesh Bhatia, Vishwa Mohan Katoch, Hajime Inoue
DOI
:10.4103/ijmr.IJMR_1980_17
PMID
:31219072
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REVIEW ARTICLES
Antimicrobial susceptibility profile & resistance mechanisms of Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens from India
p. 87
Balaji Veeraraghavan, Kamini Walia
DOI
:10.4103/ijmr.IJMR_214_18
PMID
:31219073
Antimicrobial resistance is a major concern globally. Infections due to drug-resistant pathogens are becoming difficult and a challenge to treat. As treatment choices are limited due to the high-drug resistance rates, there is an increase in the health care cost, duration of hospital stay, morbidity and mortality rates. Understanding the true burden of antimicrobial resistance for a geographical location is important to guide effective empirical therapy. To have a national data, it is imperative to have a systemic data capturing across the country through surveillance studies. Very few surveillance studies have been conducted in India to generate national data on antimicrobial resistance. This review aims to report the cumulative antibiogram and the resistance mechanisms of Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens from India.
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Next-generation strategy for treating drug resistant bacteria: Antibiotic hybrids
p. 97
Varsha Gupta, Priya Datta
DOI
:10.4103/ijmr.IJMR_755_18
PMID
:31219074
Resistance against nearly all antibiotics used clinically have been documented in bacteria. There is an ever-increasing danger caused by multidrug-resistant Gram-negative bacteria in both hospital and community settings. In Gram-negative bacteria, intrinsic resistance to currently available antibiotics is mainly due to overexpressed efflux pumps which are constitutively present and also presence of protective outer membrane. Combination therapy,
i.e.
, use of two or more antibiotics, was thought to be an effective strategy because it took advantage of the additive effects of multiple antimicrobial mechanisms, lower risk of resistance development and lower mortality and improved clinical outcome. However, none of the benefits were seen in
in vivo
studies. Antibiotic hybrids are being used to challenge the growing drug resistance threat and increase the usefulness of current antibiotic arsenal. Antibiotic hybrids are synthetic constructs of two molecules which are covalently linked. These could be two antibiotics or antibiotic with an adjuvant (efflux pump inhibitor, siderophore,
etc
.) which increases the access of the antibiotics to the target. The concepts, developments and challenges in the future use of antibiotic hybrids are discussed here. Majority of the studies have been conducted on fluoroquinolones and aminoglycosides molecules. The antibiotic tobramycin has the property to enhance the action of antimicrobial agents against which the multidrug-resistant Gram-negative bacteria were earlier resistant, and thus potentiating the action of legacy antibiotics. Antibiotic hybrids may have a role as the silver bullet in Gram-negative bacteria to overcome drug resistance as well as extend the spectrum of existing antibiotics
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Understanding policy dilemmas around antibiotic use in food animals & offering potential solutions
p. 107
Kamini Walia, Monica Sharma, Sonam Vijay, Bibek R Shome
DOI
:10.4103/ijmr.IJMR_2_18
PMID
:31219075
The looming concern of antimicrobial resistance (AMR) has prompted the government of many countries of the world to act upon and come up with the guidelines, comprehensive recommendations and policies concerning prudent use of antibiotics and containment of AMR. However, such initiatives from countries with high incidence of antibiotic-resistant bacteria in food animals are still in infancy. This review highlights the existing global policies on antibiotics use in food animals along with details of the various Indian policies and guidelines. In India, in spite of availability of integrated policies for livestock, poultry and aquaculture sector, uniform regulations with coordinated initiative are needed to formulate strict policies regarding antimicrobial use both in humans and animals. In an attempt to create effective framework to tackle the AMR, the Indian Council of Medical Research initiated a series of dialogues with various stakeholders and suggested various action points for urgent implementation. This review summarizes the recommendations made during the various consultations. The overarching aim of this review is to clearly delineate the action points which need to be carried out urgently to regulate the antibiotic use in animals.
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Antimicrobial resistance in the environment: The Indian scenario
p. 119
Neelam Taneja, Megha Sharma
DOI
:10.4103/ijmr.IJMR_331_18
PMID
:31219076
Antimicrobial resistance (AMR) continues to pose a significant public health problem in terms of mortality and economic loss. Health authorities of several countries including India have formulated action plans for its containment. In this fight against AMR, it is important to realize the contribution by all the following four spheres: humans, animals, food and environment. This review incorporates all the spheres of One Health concept from the Indian perspective. India has one of the highest rates of resistance to antimicrobial agents used both in humans and food animals. The environment, especially the water bodies, have also reported the presence of resistant organisms or their genes. Specific socio-economic and cultural factors prevalent in India make the containment of resistance more challenging. Injudicious use of antimicrobials and inadequate treatment of waste waters are important drivers of AMR in India. Use of sludge in agriculture, improper discard of livestock animals and aquaculture industry are considered AMR contributors in other countries but Indian data regarding these are lacking. Efforts to combat AMR have been initiated by the Indian health authorities but are still at preliminary stages. Keeping in view the challenges unique to India, future directions are proposed.
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Efflux pump inhibitors for bacterial pathogens: From bench to bedside
p. 129
Atin Sharma, Vivek Kumar Gupta, Ranjana Pathania
DOI
:10.4103/ijmr.IJMR_2079_17
PMID
:31219077
With the advent of antibiotics, bacterial infections were supposed to be a thing of past. However, this instead led to the selection and evolution of bacteria with mechanisms to counter the action of antibiotics. Antibiotic efflux is one of the major mechanisms, whereby bacteria pump out the antibiotics from their cellular interior to the external environment using special transporter proteins called efflux pumps. Inhibiting these pumps seems to be an attractive strategy at a time when novel antibiotic supplies are dwindling. Molecules capable of inhibiting these pumps, known as efflux pump inhibitors (EPIs), have been viewed as potential therapeutic agents that can rejuvenate the activity of antibiotics that are no longer effective against bacterial pathogens. EPIs follow some general mechanisms of efflux inhibition and are derived from various natural as well as synthetic sources. This review focuses on EPIs and identifies the challenges that have kept these futuristic therapeutics away from the commercial realm so far.
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Mismatch amplification mutation assay-polymerase chain reaction: A method of detecting fluoroquinolone resistance mechanism in bacterial pathogens
p. 146
Vijaya Kumar Deekshit, Kadeeja Jazeela, Gunimala Chakraborty, Anusha Rohit, Anirban Chakraborty, Indrani Karunasagar
DOI
:10.4103/ijmr.IJMR_2091_17
PMID
:31219078
The mismatch amplification assay is a modified version of polymerase chain reaction (PCR) that permits specific amplification of gene sequences with single base pair change. The basis of the technique relies on primer designing. The single nucleotide mismatch at the 3' proximity of the reverse oligonucleotide primer makes
Taq
DNA polymerase unable to carry out extension process. Thus, the primers produce a PCR fragment in the wild type, whereas it is not possible to yield a product with a mutation at the site covered by the mismatch positions on the mismatch amplification mutation assay (MAMA) primer from any gene. The technique offers several advantages over other molecular methods, such as PCR-restriction fragment length polymorphism (RFLP) and oligonucleotide hybridization, which is routinely used in the detection of known point mutations. Since multiple point mutations in the quinolone resistance determining region play a major role in high-level fluoroquinolone resistance in Gram-negative bacteria, the MAMA-PCR technique is preferred for detecting these mutations over PCR-RFLP and sequencing technology.
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SYSTEMATIC REVIEW
A systematic review of antimicrobial resistance of typhoidal
Salmonella
in India
p. 151
Carl D Britto, Jacob John, Valsan P Verghese, Andrew J Pollard
DOI
:10.4103/ijmr.IJMR_830_18
PMID
:31219079
Background & objectives
:
The temporal trends in the development of antimicrobial resistance (AMR) among
Salmonella
Typhi and
Salmonella
Paratyphi in India have not been systematically reported. We aimed to systematically review the temporal AMR trends (phenotypic and molecular mechanisms) in bacterial isolates from patients with enteric fever over two decades in India.
Methods
:
To identify trends in AMR in India, resistance patterns among 4611 individual
S
. Typhi isolates and 800
S
. Paratyphi A isolates, reported from 1992 to 2017 in 40 publications, were analysed. Molecular resistance determinants were extracted from 22 publications and also reviewed in accordance with the PRISMA guidelines. Articles were sourced using a predefined search strategy from different databases.
Results
:
The analyses suggested that multidrug-resistant (MDR) enteric fever was declining in India and being replaced by fluoroquinolone (FQ) resistance. Mutations in
gyrA
and
parC
were key mechanisms responsible for FQ resistance, whereas MDR was largely driven by resistance determinants encoded on mobile genetic elements (plasmids, transposons).
Interpretation & conclusions
:
The results reflect the effect of antimicrobial pressure which has been driving AMR in typhoidal
Salmonella
in India. Understanding these trends is important in planning future approaches to therapy, which serve as a baseline for assessment of the impact of new typhoid conjugate vaccines against these resistant organisms.
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SPECIAL REPORT
Establishing Antimicrobial Resistance Surveillance & Research Network in India: Journey so far
p. 164
Kamini Walia, Jayaprakasam Madhumathi, Balaji Veeraraghavan, Arunaloke Chakrabarti, Arti Kapil, Pallab Ray, Harpreet Singh, Sujatha Sistla, VC Ohri
DOI
:10.4103/ijmr.IJMR_226_18
PMID
:31219080
The Indian Council of Medical Research, in 2013, initiated the Antimicrobial Resistance Surveillance & Research Network (AMRSN) to enable compilation of data on six pathogenic groups on antimicrobial resistance from the country. The overarching aim of this network was to understand the extent and pattern of antimicrobial resistance (AMR) and use this evidence to guide strategies to control the spread of AMR. This article describes the conception and implementation of this AMR surveillance network for India. Also described are the challenges, limitations and benefits of this approach. Data from the Network have shown increasing resistance in Gram-negative bacteria in the hospitals that are part of this network. Combined resistance to third-generation cephalosporins and fluoroquinolones and increasing carbapenem resistance are worrisome, as it has an important bearing on the patients' outcome and thus needs to be addressed urgently. Data generated through this Network have been used to develop treatment guidelines, which will be supportive in harmonizing treatment practices across the tertiary level healthcare institutions in the country. While, the major benefit of having a surveillance system is the collection of real-time accurate data on AMR including the mechanisms of resistance, representativeness to community, sustaining the current effort and expanding the current activities to next levels of healthcare settings are the major challenges. The data emanating from the network besides providing evidence, expose several gaps and lacunae in the ecosystem and highlight opportunities for action by multiple stakeholders.
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POLICY DOCUMENT
Policy document on antimicrobial stewardship practices in India
p. 180
Kamini Walia, VC Ohri, Jayaprakasam Madhumathi, V Ramasubramanian
DOI
:10.4103/ijmr.IJMR_147_18
PMID
:31219081
Antimicrobial resistance (AMR) in India has become a great threat because of high rate of infectious diseases. One of the key contributing factors is high antibiotic use due to poor prescription practices, self-medication, over-the-counter sale of drugs and lack of awareness. Antimicrobial stewardship programme (AMSP) have been proved to be successful in restraining sale and use of antibiotics to a large extent in many countries. An AMSP programme for a hospital is imperative for rational and evidence-based antimicrobial therapy. The ultimate aim is to improve patient outcomes, reduce emergence of bacterial resistance and ensure longevity of the existing antimicrobials. The primary goal of AMSP is to encourage cautious use of available antibiotics by training the healthcare workers and creating awareness. This article describes the strategies and recommendations for formulation of AMSP policy for India.
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ORIGINAL ARTICLES
Susceptibility profile, resistance mechanisms & efficacy ratios of fosfomycin, nitrofurantoin & colistin for carbapenem-resistant
Enterobacteriaceae
causing urinary tract infections
p. 185
Anushree Ulhas Amladi, Baby Abirami, S Manjula Devi, Thambu David Sudarsanam, Subramani Kandasamy, Nitin Kekre, Balaji Veeraraghavan, Rani Diana Sahni
DOI
:10.4103/ijmr.IJMR_2086_17
PMID
:31219082
Background & objectives
:
The escalation in carbapenem resistance among
Enterobacteriaceae
has resulted in a lack of effective therapeutic alternatives. Older antimicrobials, fosfomycin, nitrofurantoin and colistin for urinary tract infections (UTIs) caused by carbapenem-resistant
Enterobacteriaceae
(CRE) may be effective treatment options. The objectives of this study were to evaluate the utility of fosfomycin, nitrofurantoin and colistin in treating UTI caused by CRE and molecular characterization of the plasmid-mediated carbapenem resistance mechanisms.
Methods
:
Consecutive, non-duplicate isolates of CR
Escherichia coli
and
Klebsiella
spp. from urine cultures were included (n=150). Minimum inhibitory concentrations (MIC) were determined by
E
-test (fosfomycin and nitrofurantoin) and broth microdilution (colistin). Efficacy ratios were derived by dividing susceptibility breakpoints by observed MIC values of the drugs for the isolates. Isolates were screened for genes coding for carbapenemases using multiplex PCR. Fosfomycin, nitrofurantoin and colistin-resistant isolates were screened for plasmid-borne resistance genes
fos
A3,
oqx
AB and
mcr
-1, respectively using PCR.
Results
:
Among
E. coli
, 98.9, 56 and 95 per cent isolates were susceptible to fosfomycin, nitrofurantoin and colistin, respectively, while 94 and 85 per cent of
Klebsiella
spp. were susceptible to fosfomycin and colistin, respectively. The efficacy ratios indicated fosfomycin as the drug of choice for UTI caused by CR
E. coli
and
Klebsiella
spp., followed by colistin. The
bla
NDM
gene was most common, followed by
bla
OXA48-like
. Plasmid-borne genes encoding resistance to fosfomycin, nitrofurantoin and colistin were absent.
Interpretation & conclusions
:
With increasing resistance against the current treatment options, older drugs may emerge as effective options. Molecular screening of resistant isolates is essential to prevent the spread of plasmid-borne resistance against these drugs.
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Plasmid-mediated fluoroquinolone resistance associated with extra-intestinal
Escherichia coli
isolates from hospital samples
p. 192
Shruthi S Shetty, Vijaya Kumar Deekshit, Kadeeja Jazeela, Rajeshwari Vittal, Anusha Rohit, Anirban Chakraborty, Indrani Karunasagar
DOI
:10.4103/ijmr.IJMR_2092_17
PMID
:31219083
Background & objectives
:
Infection from fluoroquinolone-resistant extra-intestinal
Escherichia coli
is a global concern. In this study, isolation and characterization of fluoroquinolone-resistant extra-intestinal
E. coli
isolates obtained from hospital samples were undertaken to detect plasmid-mediated quinolone resistance (
PMQR
) genes.
Methods
:
Forty three isolates of
E. coli
obtained from patients with extra-intestinal infections were subjected to antibiogram to detect fluoroquinolone resistance. The mechanism of fluoroquinolone resistance was determined by the detection of PMQR genes and mutations in quinolone resistance determining region (QRDR).
Results
:
Of the 43 isolates, 36 were resistant to nalidixic acid (83.72%) and 28 to ciprofloxacin (65.11%). Eight
E. coli
isolates showed total resistance to both the antimicrobials without any minimum inhibitory concentration. The detection of PMQR genes with
qnr
primers showed the presence of
qnrA
in two,
qnrB
in six and
qnrS
in 21 isolates. The gene coding for quinolone efflux pump (
qepA
) was not detected in any of the isolates tested. The presence of some unexpressed PMQR genes in fluoroquinolone sensitive isolates was also observed.
Interpretation & conclusions
:
The detection of silent PMQR genes as observed in the present study presents a risk of the transfer of the silent resistance genes to other microorganisms if present in conjugative plasmids, thus posing a therapeutic challenge to the physicians. Hence, frequent monitoring is to be done for all resistance determinants.
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Molecular characterization of colistin-resistant
Klebsiella pneumoniae
& its clonal relationship among Indian isolates
p. 199
Chaitra Shankar, Manigandan Venkatesan, Ranjani Rajan, Deepa Mani, Binesh Lal, John Antony Jude Prakash, Shalini Anandan, Agila Kumari Pragasam, Kamini Walia, VC Ohri, Balaji Veeraraghavan
DOI
:10.4103/ijmr.IJMR_2087_17
PMID
:31219084
Background & objectives
:
Klebsiella pneumoniae
(KP), a common cause of invasive infections, is often extensively drug resistant in India. At present, studies on resistance mechanism and clonal relationship of KP from India are limited. The present study was undertaken to determine the resistance mechanism and clonal relationship of colistin-resistant isolates obtained from various specimens. Carbapenemases were also determined since the isolates were carbapenem resistant.
Methods:
Sixty five isolates from blood, exudates and respiratory specimens collected between 2016 and 2017 were studied. Colistin minimum inhibitory concentration (MIC) was performed by broth-micro dilution method. Multiplex PCR was carried out to determine carbapenemases. Targeted sequencing was performed to determine mutations in
mgrB, phoP, phoQ
and multilocus sequence typing was performed to determine the prevalent clones.
Results
:
Colistin MIC ranged from 4 to 256 μg/ml. SHV, TEM and CTX-M were co-produced in 60 per cent and OXA48-like in 71 per cent. Thirteen isolates had mutations in
mgrB.
Mutations included a premature stop codon at 21
st
amino acid, the presence of insertion sequences such as IS903, IS
Kpn
14 and ISK
pn
26; and elongation of
mgrB
. Novel mutations were also observed among
phoP
and
phoQ
genes. Colistin resistance due to
mcr
genes was absent. Fifteen clonal types were seen with ST231, ST14 and ST2096 being predominant.
Interpretation & conclusions
:
This study revealed the changing trend of carbapenem resistance mechanism predominantly to OXA48-like from NDM. Known
mgrB
mutations and novel mutations in
phoP
and
phoQ
were detected. There was no plasmid-mediated colistin resistance. ST14 and ST231 were international clones associated with carbapenem resistance. Colistin-resistant KP was of diverse clones with predominantly ST231, ST14 and ST2096.
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Molecular characterization of extended-spectrum β-lactamases among clinical isolates of
Escherichia coli
&
Klebsiella pneumoniae
: A multi-centric study from tertiary care hospitals in India
p. 208
Vikas Gautam, Anjana Thakur, Megha Sharma, Avinash Singh, Shruti Bansal, Aditi Sharma, Arti Kapil, Bimal Kumar Das, Sujatha Sistla, Subhash Chandra Parija, Balaji Veeraraghavan, John Antony Jude Prakash, Kamini Walia, VC Ohri, Pallab Ray
DOI
:10.4103/ijmr.IJMR_172_18
PMID
:31219085
Background & objectives
:
The increasing prevalence of extended-spectrum β-lactamases (ESBLs) has abated therapeutic options worldwide. This study was undertaken to investigate the molecular profile and resistance patterns of ESBLs among clinical isolates of
Escherichia coli
and
Klebsiella pneumoniae
at four tertiary care centres in India.
Methods
:
Clinical isolates of
E. coli
and
K. pneumoniae
were collected from the All India Institute of Medical Sciences (AIIMS), New Delhi; the Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry; Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh and Christian Medical College (CMC), Vellore, over one and a half year period. Antimicrobial susceptibility was determined by Kirby-Bauer disc diffusion method. ESBLs were confirmed phenotypically, and multiplex PCR was performed to identify genes for β-lactamases (
bla
TEM
,
bla
SHV
,
bla
OXA-1
,
bla
CTXM-1
,
bla
CTXM-2
,
bla
CTXM-9
and
bla
CTXM-15
).
Results
:
Among 341
E. coli
isolates collected during the study period, 171 (50%) harboured
bla
TEM
, 145 (43%)
bla
OXA-1
,
70 (21%)
bla
CTXM-1
, 19 (6%)
bla
SHV
and four (1%) harboured
bla
CTXM-2
. Phenotypically, combined disc test detected ESBL production in 98/298 (33%)
E. coli
. Among 304
K. pneumoniae
isolates, 115 (38%), 89 (29%), 83 (27%), 64 (21%) and two (0.6%) harboured
bla
TEM
,
bla
OXA-1
,
bla
CTXM-1
,
bla
SHV
and
bla
CTXM-2
, respectively. Combined disc test (CDT) detected ESBL production in 42 per cent
K. pneumoniae
. Most of the
bla
CTXM-1
positive isolates were also
bla
CTXM-15
positive. The carbapenem susceptibility ranged from 56 to 88 per cent for
E. coli
and from 20 to 61 per cent for
K. pneumoniae
. Antibiotic sensitivity patterns showed that colistin (CST) was the most sensitive drug for both
E. coli
(271/274, 99%) and
K. pneumoniae
(229/234, 98%).
Interpretation & conclusions
:
The prevalence of ESBL among four study centres varied, and
bla
TEM,
bla
OXA-1
and
bla
CTXM-15
were the most common genotypes in
E. coli
and
K. pneumoniae
isolates in India. The growing carbapenem resistance and emerging colistin resistance warrant the judicious use of these antimicrobials.
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Phenotypic & genotypic profile of antimicrobial resistance in
Pseudomonas
species in hospitalized patients
p. 216
Vijeta Bajpai, Aishwarya Govindaswamy, Surbhi Khurana, Priyam Batra, Anjana Aravinda, Omika Katoch, Fahmi Hasan, Rajesh Malhotra, Purva Mathur
DOI
:10.4103/ijmr.IJMR_1_18
PMID
:31219086
Background & objectives
:
Nosocomial infections caused by multidrug-resistant,
Pseudomonas
species have become a major clinical and public health concern. The aim of this study was to characterize phenotypic and genotypic profile of antimicrobial resistance (AMR) in
Pseudomonas
spp. isolated from hospitalized patients.
Methods
:
A total of 126 consecutive, non-duplicate isolates of
Pseudomonas
spp. isolated from various clinical samples were included in the study over a period of two years. Identification and antimicrobial sensitivity was performed using automated culture system according to the Clinical and Laboratory Standards Institute (CLSI) recommendations. Phenotypic detection of extended-spectrum β-lactamases (ESBLs), Amp-C β-lactamase (AmpC) and metallo-β-lactamases (MBLs) were done by various combinations of disc-diffusion and
E
-test methods, followed by polymerase chain reaction-based detection of β-lactamase-encoding genes.
Results
:
Among 126 clinical isolates, 121 (96.1%) isolates were identified as
Pseudomonas aeruginosa
. Most of the isolates were recovered from pus sample, 35 (27.8%) followed by urine, 25 (19.84%); endotracheal aspirate, 24 (19.04%); blood, 14 (11.11%) and sputum, four (3.17%). The highest rate of resistance was against ticarcillin-clavulanic acid, 113 (89.7%) followed by meropenem, 92 (72.5%) and ceftazidime, 91 (72.3%). Overall, ESBLs, AmpC and carbapenemase production was detected in 109 (96.4%), 64 (50.8%) and 105 (94.6%) isolates by phenotypic methods. The most prevalent ESBL gene was
bla
TEM
in 72 (57.1%) and the least prevalent was
bla
SHV
in 19 (15.1%) isolates. AmpC gene was seen less compared to ESBL gene. The most prevalent carbapenemases gene was
bla
NDM-1
41 (46.06%) followed by
bla
VIM
and
bla
OXA-1
.
Interpretation & conclusions
:
Our findings suggested that a high rate of ESBLs and carbapenemases production was observed in
Pseudomonas
spp. Therefore, phenotypic and genotypic detection of AMR needs to be combined for better characterization of resistance patterns in
Pseudomonas
spp.
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Plasmid profiles among some ESKAPE pathogens in a tertiary care centre in south India
p. 222
Naveen Kumar Devanga Ragupathi, Yamuna Devi Bakthavatchalam, Purva Mathur, Agila Kumari Pragasam, Kamini Walia, VC Ohri, Balaji Veeraraghavan
DOI
:10.4103/ijmr.IJMR_2098_17
PMID
:31219087
Background & objectives
:
Plasmid has led to increase in resistant bacterial pathogens through the exchange of antimicrobial resistance (AMR) genetic determinants through horizontal gene transfer. Baseline data on the occurrence of plasmids carrying AMR genes are lacking in India. This study was aimed to identify the plasmids associated with AMR genetic determinants in ESKAPE pathogens.
Methods
:
A total of 112 ESKAPE isolates including
Escherichia coli
(n=37),
Klebsiella pneumoniae
(n=48, including 7 pan-drug susceptible isolates),
Acinetobacter baumannii
(n=8),
Pseudomonas aeruginosa
(n=1) and
Staphylococcus aureus
(n=18) were analyzed in the study. Isolates were screened for antimicrobial susceptibility and whole genome sequencing of isolates was performed using Ion Torrent (PGM) sequencer. Downstream data analysis was done using PATRIC, ResFinder, PlasmidFinder and MLSTFinder databases. All 88 whole genome sequences (WGS) were deposited at GenBank.
Results
:
Most of the study isolates showed resistant phenotypes. As analyzed from WGS, the isolates included both known and unknown sequence types. The plasmid analysis revealed the presence of single or multiple plasmids in the isolates. Plasmid types such as IncHI1B(pNDM-MAR), IncFII(pRSB107), IncFIB(Mar), IncFIB(pQil), IncFIA, IncFII(K), IncR, ColKP3 and ColpVC were present in
K. pneumoniae
. In
E. coli
, IncFIA, IncFII, IncFIB, Col(BS512), IncL1, IncX3 and IncH were present along with other types.
S. aureus
harboured seven different plasmid groups pMW2 (
rep
5), pSAS1 (
rep
7), pDLK1 (
rep
10), pUB110 (
rep
US12), Saa6159 (
rep
16), pKH12 (
rep
21) and pSA1308 (
rep
21). The overall incidence of IncF type plasmids was 56.5 per cent followed by Col type plasmids 18.3 per cent and IncX 5.3 per cent. Other plasmid types identified were <5 per cent.
Interpretation & conclusions
:
Results from the study may serve as a baseline data for the occurrence of AMR genes and plasmids in India. Information on the association between phenotypic and genotypic expression of AMR was deciphered from the data. Further studies on the mechanism of antibiotic resistance dissemination are essential for enhancing clinical lifetime of antibiotics.
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Phenotypic & genotypic study of antimicrobial profile of bacteria isolates from environmental samples
p. 232
Santhosh Kogaluru Shivakumaraswamy, Vijaya Kumar Deekshit, Rajeshwari Vittal, Dharnappa Sannejal Akhila, Dechamma Muthappa Mundanda, Juliet Roshini Mohan Raj, Anirban Chakraborty, Indrani Karunasagar
DOI
:10.4103/ijmr.IJMR_2097_17
PMID
:31219088
Background & objectives
:
The resistance to antibiotics in pathogenic bacteria has increased at an alarming rate in recent years due to the indiscriminate use of antibiotics in healthcare, livestock and aquaculture. In this context, it is necessary to monitor the antibiotic resistance patterns of bacteria isolated from the environmental samples. This study was conducted to determine the phenotypic and genotypic profile of antimicrobial resistance in Gram-negative bacteria isolated from environmental samples.
Methods
:
Two hundred and fifty samples were collected from different sources,
viz
. fish and fishery products (99), livestock wastes (81) and aquaculture systems (70), in and around Mangaluru, India. Isolation, identification and antimicrobial profiling were carried out as per standard protocols. The isolates were screened for the presence of resistance genes using PCR.
Results
:
A total of 519 Gram-negative bacteria comprising
Escherichia coli
(116),
Salmonella
spp. (14),
Vibrio
spp. (258),
Pseudomonas
spp. (56),
Citrobacter
spp. (26) and
Proteus
spp. (49) were isolated and characterized from 250 samples obtained from different sources. A total of 12 antibiotics were checked for their effectiveness against the isolates. While 31.6 per cent of the isolates were sensitive to all the antibiotics used, 68.4 per cent of the isolates showed resistance to at least one of the antibiotics used. One-third of the isolates showed multidrug resistance. Maximum resistance was observed for ampicillin (43.4%), followed by nitrofurantoin (20.8%). Least resistance was seen for carbapenems and chloramphenicol. PCR profiling of the resistant isolates confirmed the presence of resistance genes corresponding to their antibiotic profile.
Interpretation & conclusions
:
This study results showed high rate of occurrence of antimicrobial resistance and their determinants in Gram-negative bacteria isolated from different environmental sources.
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Molecular characterization & epidemiology of carbapenem-resistant
Acinetobacter baumannii
collected across India
p. 240
Saranya Vijayakumar, Purva Mathur, Arti Kapil, Bimal K Das, Pallab Ray, Vikas Gautam, Sujatha Sistla, Subhash Chandra Parija, Kamini Walia, VC Ohri, Shalini Anandan, Kandasamy Subramani, Iyyadurai Ramya, Balaji Veeraraghavan
DOI
:10.4103/ijmr.IJMR_2085_17
PMID
:31219089
Background & objectives
:
Acinetobacter baumannii
is an opportunistic pathogen responsible for causing nosocomial infections.
A. baumannii
develops resistance to various antimicrobial agents including carbapenems, thereby complicating the treatment. This study was performed to characterize the isolates for the presence of various β-lactamases encoding genes and to type the isolates to compare our clones with the existing international clones across five centres in India.
Methods
:
A total 75 non-repetitive clinical isolates of
A. baumannii
from five different centres were included in this study. All the isolates were confirmed as
A. baumannii
by
bl
a
OXA-51-like
PCR. Multiplex PCR was performed to identify the presence of extended spectrum β-lactamases (ESBL) and carbapenemases. Multilocus sequence typing was performed to find the sequence type (ST) of the isolates. e-BURST analysis was done to assign each ST into respective clonal complex.
Results
:
bla
OXA-51-like
was present in all the 75 isolates. The predominant Class D carbapenemase was
bla
OXA-23-like
followed by Class B carbapenemase,
bla
NDM-like
. Class A carbapenemase was not observed.
bla
PER-like
was the predominant extended spectrum β-lactamase. ST-848, ST-451 and ST-195 were the most common STs. Eight-novel STs were identified. e-BURST analysis showed that the 75
A. baumannii
isolates were clustered into seven clonal complexes and four singletons, of which, clonal complex 208 was the largest.
Interpretation & conclusions
:
Most of the isolates were grouped under clonal complex 208 which belongs to the international clonal lineage 2. High occurrence of ST-848 carrying
bla
OXA-23-like
gene suggested that ST-848 could be an emerging lineage spreading carbapenem resistance in India.
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Antimicrobial resistance, virulence & plasmid profiles among clinical isolates of
Shigella
serogroups
p. 247
Dhiviya Prabaa Muthuirulandi Sethuvel, Susmitha Perumalla, Shalini Anandan, Joy Sarojini Michael, Naveen Kumar Devanga Ragupathi, Revathi Gajendran, Kamini Walia, Balaji Veeraraghavan
DOI
:10.4103/ijmr.IJMR_2077_17
PMID
:31219090
Background & objectives
:
Bacillary dysentery caused by
Shigella
spp. remains an important cause of the crisis in low-income countries. It has been observed that
Shigella
species have become increasingly resistant to most widely used antimicrobials. In this study, the antimicrobial resistance, virulence and plasmid profile of clinical isolates of
Shigella
species were determined.
Methods
:
Sixty clinical
Shigella
isolates were subjected to whole-genome sequencing using Ion Torrent platform and the genome sequences were analyzed for the presence of acquired resistance genes, virulence genes and plasmids using web-based software tools.
Results
:
Genome analysis revealed more resistance genes in
Shigella flexneri
than in other serogroups. Among β-lactamases,
bla
OXA-1
was predominantly seen followed by the
bla
TEM-1B
and
bla
EC
genes. For quinolone resistance, the
qnr
S gene was widely seen. Novel mutations in
gyr
B,
par
C and
par
E genes were observed. Cephalosporins resistance gene,
bla
CTX-M-15
was identified and plasmid-mediated AmpC β-lactamases genes were found among the isolates. Further, a co-trimoxazole resistance gene was identified in most of the isolates studied. Virulence genes such as
ipaD
,
ipaH
,
virF
,
senB
,
iha
,
capU
,
lpfA
,
sigA
,
pic
,
sepA
,
celb
and
gad
were identified. Plasmid analysis revealed that the IncFII was the most commonly seen plasmid type in the isolates.
Interpretation & conclusions
:
The presence of quinolone and cephalosporin resistance genes in
Shigella
serogroups has serious implications for the further spread of this resistance to other enteric pathogens or commensal organisms. This suggests the need for continuous surveillance to understand the epidemiology of the resistance.
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Presence of extracellular DNA & protein in biofilm formation by gentamicin-resistant
Lactobacillus plantarum
p. 257
Jaimee George, Prakash Motiram Halami
DOI
:10.4103/ijmr.IJMR_2022_17
PMID
:31219091
Background & objectives
:
Bacterial biofilms a multi-layered defence, comprise extracellular DNA (eDNA) and proteins, protect bacteria from harmful environment and nutrient limitation and utilize the mutual benefits within a community. Bacterial biofilms also defend bacteria from harsh environments such as antibiotic treatment. This leads to poor antibiotic penetration, slow growth, adaptive stress responses, and formation of persister cells. This study was done to determine the relation of antibiotic resistance deciphered by the biofilms in
Lactobacillus plantarum
, a lactic acid bacteria (LAB) with probiotic significance.
Methods
:
The gentamicin-resistant
L. plantarum
isolates were allowed to form biofilms and subjected to DNase I and proteinase K treatment. The optical density (OD) values were recorded for the biofilm assay and the cell count for the number of viable cells was taken for the control and the test samples. Percentage reduction was calculated based on the difference between the initial and final OD for both the parameters.
Results
:
The biofilm assay revealed that the native
L. plantarum
isolates which were phenotypically susceptible, possessed the ability to form biofilms. The OD values were significantly decreased in comparison to the biofilm-forming control culture when these were treated with DNase I and proteinase K.
Interpretation & conclusions
:
The study revealed that the biofilms formed by
L. plantarum
comprised of eDNA and proteins which was evidenced by the reduction in OD values and percentage in comparison to the control upon DNase I and proteinase K treatment. This indicates that the eDNA and biofilm matrix proteins are vital constituents of biofilms and may carry significant risk when coupled with antibiotic resistance.
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Current antibiotic use in the treatment of enteric fever in children
p. 263
Sushila Dahiya, Rooma Malik, Priyanka Sharma, Archana Sashi, Rakesh Lodha, Sushil Kumar Kabra, Seema Sood, Bimal Kumar Das, Kamini Walia, VC Ohri, Arti Kapil
DOI
:10.4103/ijmr.IJMR_199_18
PMID
:31219092
Background & objectives
:
Antimicrobial resistance is a major challenge in the treatment of typhoid fever with limited choices left to empirically treat these patients. The present study was undertaken to determine the current practices of antibiotic use in children attending a tertiary care hospital in north India.
Methods
:
This was a descriptive observational study in children suffering from enteric fever as per the case definition including clinical and laboratory parameters. The antibiotic audit in hospitalized children was measured as days of therapy per 1000 patient days and in outpatient department (OPD) as antibiotic prescription on the treatment card.
Results
:
A total of 128 children with enteric fever were included in the study, of whom, 30 were hospitalized and 98 were treated from OPD. The mean duration of fever was 9.5 days at the time of presentation. Of these, 45 per cent were culture positive with
Salmonella
Typhi being aetiological agent in 68 per cent followed by
S
. Paratyphi A in 32 per cent. During hospitalization, the average length of stay was 10 days with mean duration of defervescence 6.4 days. Based on antimicrobial susceptibility ceftriaxone was given to 28 patients with mean duration of treatment being six days. An additional antibiotic was needed in six patients due to clinical non-response. In OPD, 79 patients were prescribed cefixime and additional antibiotic was needed in five during follow up visit.
Interpretation & conclusions
:
Based on our findings, ceftriaxone and cefixime seemed to be the first line of antibiotic treatment for typhoid fever. Despite susceptibility, clinical non-response was seen in around 10 per cent of the patients who needed combinations of antibiotics.
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Heterogeneity of macrolide-lincosamide-streptogramin phenotype & conjugal transfer of
erm
(B) in
Pediococcus pentosaceus
p. 270
Surya Chandra Rao Thumu, Prakash M Halami
DOI
:10.4103/ijmr.IJMR_2055_17
PMID
:31219093
Background & objectives
:
Pediococcus pentosaceus
has been reported to cause clinical infections while it is being promoted as probiotic in food formulations. Antibiotic resistance (AR) genes in this species are a matter of concern for treating clinical infections. The present study was aimed at understanding the phenotypic resistance of
P. pentosaceus
to macrolide-lincosamide-streptogramin B (MLS
B
) antibiotics and the transfer of AR to pathogens.
Methods
:
P. pentosacues
isolates (n=15) recovered from fermented foods were screened for phenotypic resistance to MLS
B
antibiotics using disc diffusion and microbroth dilution methods. Localization and transferability of the identified resistance genes,
erm
(B) and
msr
(C) were evaluated through Southern hybridization and
in vitro
conjugation methods.
Results
:
Four different phenotypes; sensitive (S) (n=5), macrolide (M) (n=7), lincosamide (L) (n=2) and constitutive (cMLS
B
) (n=1) were observed among the 15
P. pentosaceus
isolates. High-level resistance (>256 μg/ml) to MLS
B
was observed with one cMLS
B
phenotypic isolate IB6-2A. Intermediate resistance (8-16 μg/ml) to macrolides and lincosamides was observed among M and L phenotype isolates, respectively. Cultures with S phenotype were susceptible to all other antibiotics but showed unusual minimum inhibitory concentration (MIC) values of 8-16 μg/ml for azithromycin. Southern hybridization studies revealed that resistance genes localized on the plasmids could be conjugally transferred to
Enterococcus faecalis
JH2-2.
Interpretation & conclusions
:
The study provides insights into the emerging novel resistance patterns in
P. pentosaceus
and their ability to disseminate AR. Monitoring their resistance phenotypes before use of MLS antibiotics can help in successful treatment of Pediococcal infections in humans.
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Antibiotic-resistant
Enterobacteriaceae
in healthy gut flora: A report from north Indian semiurban community
p. 276
Madhu Gupta, Gunjan Didwal, Shruti Bansal, Kanica Kaushal, Nitya Batra, Vikas Gautam, Pallab Ray
DOI
:10.4103/ijmr.IJMR_207_18
PMID
:31219094
Background & objectives
:
Rampant use of β-lactam antibiotics in both community and hospitals has transformed the human healthy intestinal gut flora into a reservoir of antibiotic-resistant organisms. This study was conducted to find the faecal presence of antibiotic-resistant
Enterobacteriaceae
in faecal samples in the community in north India.
Methods
:
In this prospective study, 207 stool samples were collected from apparently healthy individuals residing in a semiurban community in Chandigarh, India, from August to October, 2015. Isolates belonging to family
Enterobacteriaceae
were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and antibiotic susceptibility was determined using Clinical Laboratory Standard Institute disc diffusion method. Detection of extended spectrum β-lactamases (TEM, SHV, OXA-1, CTXM 1, CTXM 2, CTXM 9 and CTXM 8/25), carbapenemases (IMP, VIM and KPC) and New Delhi metallo-β-lactamase was done by multiplex PCR.
Results
:
Of the population studied, 55.5 per cent were females and 60 per cent were illiterate or had only primary education; 43.4 per cent individuals were aged <20 yr. Overall, 70.5 per cent of stool samples had antibiotic-resistant isolates. Maximum resistance was seen for cephalosporins (60.4%) followed by fluoroquinolones (41.5%). The multidrug-resistant (MDR) isolates were 2.4 per cent. The most commonly detected genes were TEM, SHV, OXA-1, CTXM-1, CTXM-2, CTXM-9 and CTXM-8/25 β-lactamases.
Escherichia coli
was the most common resistant isolate, and TEM was the most common gene detected.
Interpretation & conclusions
:
Overall, 70.5 per cent members of
Enterobacteriaceae
had antibiotic resistance in the community and 2.4 per cent were MDR. Higher resistance rates were observed for most commonly used drugs such as cephalosporins and fluoroquinolones. High rate of antibiotic-resistant
Enterobacteriaceae
in gut of healthy individuals points towards the need for active screening and prevention of dissemination.
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CTX-M type extended-spectrum β-lactamase in
Escherichia coli
isolated from extra-intestinal infections in a tertiary care hospital in south India
p. 281
Anusha Rohit, Vijaya Kumar Deekshit, Malathi Balaraj, Veena Shetty Alandur, Georgi Abraham, Iddya Karunasagar, Indrani Karunasagar
DOI
:10.4103/ijmr.IJMR_2099_17
PMID
:31219095
Background & objectives
:
Infections caused by extended-spectrum β-lactamase (ESBL)-producing
Escherichia coli
carrying
bla
CTX-M
genes have been spreading globally, but there are geographical variations in the type of
bla
CTX-M
genes prevalent and there are scanty data from India. This study was conducted to determine the CTX-M type ESBLs in
E. coli
isolates obtained from clinical specimens from patients with extra-intestinal infections attending a tertiary care hospital in south India.
Methods
:
ESBL-producing
E. coli
isolated from patients with extra-intestinal infections were subjected to PCR using CTX-M group-specific primers. From a representative isolate, full-length
CTX-M-15
gene was amplified and sequenced. An internal fragment of this gene was sequenced in 10 representative isolates.
Results
:
Of the 300 isolates of
E. coli
tested, 88 per cent carried
CTX-M
genes and
bla
CTX-M-15
was the most dominant gene present in 90 per cent of the positive isolates. Most (91%) of the isolates positive for
bla
CTX-M
were sensitive to meropenem.
Interpretation & conclusions
:
Our findings showed
bla
CTX-M-15
to be the dominant gene. Based on the data on antimicrobial susceptibility, cefoperazone-sulbactum could be an antimicrobial of choice.
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Molecular epidemiology & therapeutic options of carbapenem-resistant Gram-negative bacteria
p. 285
Atul Garg, Jaya Garg, Sachin Kumar, Amitabh Bhattacharya, Saurabh Agarwal, GC Upadhyay
DOI
:10.4103/ijmr.IJMR_36_18
PMID
:31219096
Background & objectives
:
The growing incidence and the wide diversity of carbapenemase-producing bacterial strains is a major concern as only a few antimicrobial agents are active on carbapenem-resistant bacteria. This study was designed to study molecular epidemiology of carbapenem-resistant Gram-negative bacterial (GNB) isolates from the community and hospital settings.
Methods
:
In this study, non-duplicate GNB were isolated from clinical specimens, and phenotypic test such as modified Hodge test, metallo β-lactamase E-strip test,
etc
. were performed on carbapenem-resistant bacteria. Multiplex PCR was performed to identify the presence of
bla
IMP
,
bla
VIM
,
bla
KPC
,
bla
OXA48
,
bla
OXA23
,
bla
SPM
,
bla
GIM
,
bla
SIM
and
bla
NDM
. Minimum inhibitory concentration (MIC) of colistin, fosfomycin, minocycline, chloramphenicol and tigecycline was also determined.
Results
:
Of the 3414 GNB studied, carbapenem resistance was 9.20 per cent and maximum resistance (11.2%) was present at tertiary care centre, followed by secondary care (4%) and primary centre (2.1%). Among the carbapenem-resistant bacteria, overall, the most common isolate was
Pseudomonas aeruginosa
(24%). On multiplex PCR 90.3 per cent carbapenem-resistant isolates were positive for carbapenemase gene. The
bla
NDM
(63%) was the most prevalent gene followed by
bla
VIM
(18.4%). MIC results showed that 88 per cent carbapenem-resistant
Enterobacteriaceae
were sensitive to fosfomycin, whereas 78 per cent of
P. aeruginosa
and 85 per cent
Acinetobacter
spp. were sensitive to colistin.
Interpretation & conclusions
:
Carbapenem resistance in GNB isolates from the community and hospital settings was found to be on the rise and should be closely monitored. In the absence of new antibiotics in pipeline and limited therapeutic options, prudent use of antibiotics and strict infection control practices should be followed in hospital to limit the emergence and spread of multidrug-resistant bacteria.
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Presence & mobility of antimicrobial resistance in Gram-negative bacteria from environmental samples in coastal Karnataka, India
p. 290
Juliet Roshini Mohan Raj, Rajeshwari Vittal, Santhosh Kogaluru Shivakumaraswamy, Vijaya Kumar Deekshit, Anirban Chakraborty, Indrani Karunasagar
DOI
:10.4103/ijmr.IJMR_2088_17
PMID
:31219097
To understand antimicrobial resistance (AMR) patterns and mechanisms of horizontal gene transfer in human-associated environments is essential to AMR surveillance. Gram-negative bacteria (1122 isolates) from food-animal environments were characterized for antimicrobial susceptibility and AMR genes. Seventy five per cent of the isolates (837 of 1122) were resistant to at least one of the antibiotics tested. Resistance to more than three groups of antimicrobials (multidrug resistance) was observed in 43 isolates with most often encountered (12 of 43) resistance to β-lactams, tetracycline, quinolones and nitrofurantoin. The profile of frequently reported plasmid-mediated resistance gene in these isolates was determined. The mobility of these elements as plasmids or phages was examined. The
bla
CTX-M
gene was present in the plasmid of 61 per cent and packed in induced phage fractions in 72 per cent of the isolates and
bla
TEM
in 69 per cent phage fractions compared to 15 per cent presence in the plasmid.
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Pathogen burden & associated antibiogram of
Pseudomonas
spp. in a tertiary care hospital of India
p. 295
Minu Kumari, Surbhi Khurana, Nidhi Bhardwaj, Rajesh Malhotra, Purva Mathur
DOI
:10.4103/ijmr.IJMR_14_18
PMID
:31219098
Antimicrobial resistance particularly in Gram-negative bacilli is an increasing problem worldwide.
Pseudomonas
spp. is one the most common Gram-negative bacteria associated with nosocomial infections and therefore, its trend of antimicrobial resistance needs to be studied. The aim of this study was to evaluate the rate of antimicrobial resistance and changes in resistance pattern over a period of five years (2012-2016) in
Pseudomonas
spp. isolated from trauma patients attending a tertiary care hospital in north India. During the study, a total of 2444
Pseudomonas
spp. were isolated from the various clinical sample. The most common species isolated was
P. aeruginosa
(2331, 95%). The highest level of resistance was observed against levofloxacin (1678, 69%) and the lowest level of resistance was observed against tobramycin (1254, 51%). Irrational and inappropriate use of antibiotics was found to be responsible for multidrug resistance in
Pseudomonas
spp. Hence, there is an urgent need to emphasize strict antibiotic policy to minimize the misuse of antimicrobials.
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Developing a hybrid antimicrobial resistance surveillance system in India: Needs & challenges
p. 299
Jasmine Kaur, Arun Sharma, Ajay Singh Dhama, Harish Buttolia, VC Ohri, Kamini Walia, Amitesh Kumar Sharma, Koji Yahara, Rafi Ahmad, Harpreet Singh
DOI
:10.4103/ijmr.IJMR_2074_17
PMID
:31219099
Growing resistance to antimicrobials has become one of the most important problems of the 21
st
century. The development of new antibiotics is a time-consuming process involving huge financial resources. An alternate approach is proper utilization of the existing antibiotics through the surveillance of resistance. An important component of surveillance is the informatics tool for collection, management and analysis of antimicrobial resistance susceptibility testing data. Based on the scope, antimicrobial resistance surveillance resistance tools can be broadly classified as collectors and integrators. Individually, both the integrators and collectors have limitations which restrict their use in India. There is a strong requirement to develop a hybrid AMR surveillance tool that captures standardized data from small laboratories and integrates data from multiple sources to present a complete picture of the country. Here we describe a tool
i
-AMRSS developed by the Indian Council of Medical Research for collection, storage and management of AMR data from collaborating institutes/laboratories and to generate real-time analytics and reports.
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CORRESPONDENCE
Role of phenotypic testing in determining the mechanism of resistance in Gram-negative bacilli & risk factors for meropenem resistance
p. 303
Kavita Raja, Molly Antony, Reeja Rani, Gracyamma Bridget
DOI
:10.4103/ijmr.IJMR_545_18
PMID
:31219100
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