Chaitra Shankar - Academia.edu (original) (raw)

Papers by Chaitra Shankar

Research paper thumbnail of In vitro activity of β-lactam-β-lactam enhancer combination, cefepime/zidebactam (WCK 5222, FEP/ZID) against multi-clonal, colistin-resistant Klebsiella pneumoniae

International Journal of Antimicrobial Agents, Sep 1, 2021

Research paper thumbnail of Emergence of Multidrug Resistant Hypervirulent ST23 Klebsiella pneumoniae: Multidrug Resistant Plasmid Acquisition Drives Evolution

Frontiers in Cellular and Infection Microbiology, Nov 20, 2020

Background: In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MD... more Background: In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used the complete genome sequence of two MDR hvKp isolates belonging to ST23 to characterize the phylogenetic background and plasmid diversity. Methods: Two hvKp isolates from patients with bacteremia were sequenced using Ion Torrent PGM and Oxford Nanopore MinION platforms and assembled by hybrid genome assembly approach. Comparative genomics approaches were used to investigate the population structure, evolution, virulence, and antimicrobial resistance of MDR hvKp strains. Results: The study isolates exhibited typical features of hvKp phenotypes associated with ST23. The convergence of multidrug resistance and hypervirulence were attributed by the presence of multiple plasmids including a 216 kb virulence plasmid and MDR plasmids belonging to IncA/C 2 , IncFIB, IncX3, and ColKP3 groups. The insertion of catA1 gene into virulence plasmid was observed along with genetic factors such as aerobactin, salmochelin, and rmpA2 that confer hvKp's hypervirulent phenotype. The core genome single nucleotide polymorphism (SNP) phylogenetic analyses of the isolates showed the evolution of ST23 hvKp was predominantly driven by ICEKp acquisitions. Conclusion: To the best of our knowledge, this is the first report of MDR hvKp isolates of ST23 with insertion of catA1 gene into the virulence plasmid which presents the possibility of hotspot integration sites on the plasmids to aid acquisition of AMR genes. ST23 is no longer confined to susceptible strains of hvKp. Our findings emphasize the need for more studies on recombinant events, plasmid transmission dynamics and evolutionary process involving hvKp.

Research paper thumbnail of Genomic insights into multi-drug and extensively drug resistant Klebsiella pneumoniae from India

International Journal of Infectious Diseases, Dec 1, 2020

Research paper thumbnail of Bad Bug, No Test: Tigecycline Susceptibility Testing Challenges and Way Forward

Indian Journal of Medical Microbiology, 2019

There is a drastic increase in the incidence of extensively drug-resistant Gram-negative bacteria... more There is a drastic increase in the incidence of extensively drug-resistant Gram-negative bacteria in the recent times, especially in India. Klebsiella pneumoniae and Acinetobacter baumannii are the two most common pathogens with high drug-resistant rates of up to 40% and 70% carbapenem resistance, respectively. [1] Very few agents are available for the management of these drug-resistant infections. Tigecycline and colistin are the drugs of last resort for treatment as single agents/in combination with other antibiotics. However, both these agents have shortcomings in terms of susceptibility testing, which significantly impact on its right use. Tigecycline is approved for the treatment of Gram-positive and Gram-negative bacteria causing intra-abdominal infections and skin and soft tissue infections. [2] However, it is used off-label for the treatment of other infections such as septicaemia. Tigecycline is a reserve antibiotic increasingly used for the treatment of multidrug-resistant bacteria, especially Klebsiella pneumoniae and Acinetobacter baumannii. At present, there are concerns regarding the testing and interpretation of tigecycline susceptibility to bugs such as K. pneumoniae and A. baumannii, which limit clinicians in appropriate usage. Use of appropriate method for testing such as broth microdilution is essential. In addition, tigecycline susceptibility testing is a challenge due to inconsistent results from various antimicrobial susceptibility testing automated platforms. There is a great need to define a suitable methodology along with interpretive criteria, especially for K. pneumoniae and A. baumannii. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Food and Drug Administration (FDA) breakpoints show wide variation and are defined for different set of organisms. Non-species-related pharmacokinetic/pharmacodynamic (PK/ PD) breakpoints defined by the EUCAST can be used for organisms such as K. pneumoniae and A. baumannii.

Research paper thumbnail of Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096 <i>Klebsiella pneumoniae</i> in India: The rise of a new superbug?

Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also... more Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed to characterise nine novel MDR hvKp isolates harbouring mosaic plasmids simultaneously carrying antimicrobial resistance (AMR) and virulence genes. Nine HvKp isolates obtained from hospitalised patients in southern India were characterized for antimicrobial susceptibility and hypervirulence phenotypes. All nine hvKp isolates were subjected to whole genome sequencing (WGS) using Ilumina HiSeq2500 and a subset of four were sequenced using Oxford Nanopore MinION. Among the nine isolates, seven were carbapenem-resistant, two of which carried bla NDM-5 on an IncFII plasmid and five carried bla OXA-232 on a ColKP3 plasmid. The virulence determinants were encoded in a mosaic plasmid (~320 Kbp) that formed as a result of its insertion in a IncFIB-IncHI1B plasmid co-integrate. The mosaic plasmid carried AMR genes (aadA2, armA, blaOXA-1, msrE, mphE, sul1 and dfrA14) in addition to rmpA2, iutA and iucABCD virulence genes. Interestingly the mosaic plasmid carried its own type IV-A3 CRISPR-cas system that is likely able to target the acquisition of IncF plasmid with the help of a traL spacer. The convergence of virulence and AMR is the biggest threat among invasive K. pneumoniae infections. However, increasing reports of the presence of mosaic plasmid carrying both AMR and virulence genes suggests MDR-hvKp isolates are no longer confined to selected clones and the containment of such isolates is very challenging. IMPORTANCE Klebsiella pneumoniae is an opportunistic pathogen that commonly associated with hospital-acquired infections in the urinary tract, respiratory tract, lung, wound sites. The organism has gained notoriety by acquiring additional genetic traits to become either hypervirulent (HV) phenotype or multidrug resistant (MDR) phenotype. Though the infections by both these phenotypes were very challenging to treat, the MDR K. pneumonia (MDR-Kp) were remained in the hospital settings while HV K. pneumonia (hvKp) strains were mostly originated from the community settings. In a recent turn of events, the evolution of MDR-Kp and hvKp has converged as both clones found to carry both MDR plasmids and virulence plasmid. These convergent strains are challenging to treat and is associated with higher mortality rate. As the recent hvKp isolates harbour mosaic plasmid encoding both AMR

Research paper thumbnail of First Report of Whole-Genome Sequence of Colistin-Resistant <i>Klebsiella quasipneumoniae</i> subsp. <i>similipneumoniae</i> Producing KPC-9 in India

Microbial Drug Resistance, May 1, 2019

Aim: Klebsiella pneumoniae carbapenemase (KPC) is a class A carbapenemase endemic in the United S... more Aim: Klebsiella pneumoniae carbapenemase (KPC) is a class A carbapenemase endemic in the United States, China, South America, and Europe but is rarely reported from India. A single report of KPC-9 from K. pneumoniae in Israel has been published. K. pneumoniae has been classified into three phylogenetic groups: group 1 consists of K. pneumoniae and its subspecies, group 2 consists of Klebsiella quasipneumoniae and its subspecies, and group 3 consists of Klebsiella variicola. This is the first report of whole-genome sequencing of colistin-resistant K. quasipneumoniae subsp. similipneumoniae harboring blaKPC-9 gene. Results: The isolate was obtained from the culture of a respiratory catheter tip from a 41-year-old woman with traumatic brain injury. Whole-genome sequencing showed the presence of blaOKP-B-3 gene and hence it was identified as K. quasipneumoniae subsp. similipneumoniae. The isolate was resistant to all antimicrobials except tigecycline. Colistin resistance was chromosomally mediated; mcr-1 to mcr-5 genes and their variants were not identified. The isolate belonged to the novel clonal type ST2957. Conclusion: The isolation of KPC-9 from India, a nonendemic region, and in an isolate of K. quasipneumoniae highlights the importance of accurate identification of Klebsiella species and determination of mechanism of resistance. The novel sequence type obtained indicates evolution of the organism and acquisition of plasmid-mediated resistance. The occurrence of KPC in India is a potential public health threat.

Research paper thumbnail of Identification of plasmids by PCR based replicon typing in bacteremic Klebsiella pneumoniae

Microbial Pathogenesis, Nov 1, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Research paper thumbnail of Emergence of ST147 Klebsiella pneumoniae carrying bla on IncA/C2 with ompK35 and ompK36 mutations in India

Journal of Infection and Public Health, Sep 1, 2019

India is known to be endemic to NDM carbapenemases. However, NDM-7 among Klebsiella pneumoniae ha... more India is known to be endemic to NDM carbapenemases. However, NDM-7 among Klebsiella pneumoniae has not been described from India. Apart from carbapenemases, ompK35 and ompK36 also contribute to carbapenem resistance in K. pneumoniae. This study describes molecular mechanisms of antimicrobial resistance in an isolate from bacteraemia investigated through whole genome sequencing. bla NDM-7 was found on IncA/C2 plasmid which also carried sul-1, aadA2, rmtC, bla CMY-6 and ARR-2. ompK35 had mutations and changes from 39th amino acid. ompK36 was truncated to 248 amino acids. The isolate belonged to ST147. The patient was a known case systemic lupus erythematosus (SLE) and blood culture grew carbapenem resistant K. pneumoniae. Meropenem, colistin and tiecoplanin were administered and the patient was discharged on improvement. Emergence of new resistance variants and porin mutations among clones such as ST147 which has been prevalent has potential for rapid spread and thus challenges infection control.

Research paper thumbnail of Molecular characterization of colistin-resistant Klebsiella pneumoniae & its clonal relationship among Indian isolates

Indian Journal of Medical Research, 2019

Background & objectives: Klebsiella pneumoniae (KP), a common cause of invasive infections, i... more 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 21st 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.

Research paper thumbnail of Hybrid Plasmids Encoding Antimicrobial Resistance and Virulence Traits Among Hypervirulent Klebsiella pneumoniae ST2096 in India

Frontiers in Cellular and Infection Microbiology

BackgroundHypervirulent variants ofKlebsiella pneumoniae(HvKp) were typically associated with a b... more BackgroundHypervirulent variants ofKlebsiella pneumoniae(HvKp) were typically associated with a broadly antimicrobial susceptible clone of sequence type (ST) 23 at the time of its emergence. Concerningly, HvKp is now also emerging within multidrug-resistant (MDR) clones, including ST11, ST15, and ST147. MDR-HvKp either carry both the virulence and resistance plasmids or carry a large hybrid plasmid coding for both virulence and resistance determinants. Here, we aimed to genetically characterize a collection of MDR-HvKp ST2096 isolates haboring hybrid plasmids carrying both antimicrobial resistance (AMR) and virulence genes.MethodsNineK. pneumoniaeST2096 isolated over 1 year from the blood sample of hospitalized patients in southern India that were MDR and suspected to be HvKp were selected. All nine isolates were subjected to short-read whole-genome sequencing; a subset (n = 4) was additionally subjected to long-read sequencing to obtain complete genomes for characterization. Mucovi...

Research paper thumbnail of Correlation of carbapenem resistance and hypermucoviscosity in K.pneumoniae isolated from blood culture at a tertiary hospital in South India

International Journal of Infectious Diseases, 2016

efflux-pump gene expressions (marA, mdfA) were also checked for the MDR isolates. Results: Out of... more efflux-pump gene expressions (marA, mdfA) were also checked for the MDR isolates. Results: Out of 453 samples screened for E. coli, 386 (85.2%) isolates was recovered, while 47 (7.03%) Salmonella was isolated from 668 samples examined. Above 6 percent E. coli showed resistance to all the tested antibiotics. Over 80 percent Salmonella were resistant to amikacin, cefazolin and tobramycin and other remaining exhibited high frequency of resistance against cefuroxime (74.5%) and gentamicin (68.1%). Overall marA gene was the most common type with 15 percent harboring the gene. Above 10.8 percent isolates possessed sul1, sul2, tetA, strA genes and above 5 percent carried tetB, aadA, armA, bla TEM and bla CTX-M , however, bla SHV gene, armB and rmtC were not recovered. Plasmid mediated quinolone resistant gene positive strains totaled to 4.4 (qnrB) and 2.07 (qnrS) percent while qnrA was not detected. Species and region-wise distributions were variable. Resistant traits were transferable and the resistant isolates had shown ≥2 fold increase in the expression level of marA. ' Conclusion: Emergence of MDR in E. coli or Salmonella among the animal populations of NE India was evident from the study revealing above 85 percent MDR isolates. These results emphasize the urgent need for surveillance of antibiotic resistance incorporating rational and regulated use of antibiotics in Livestock farming.

Research paper thumbnail of Clinical and Genomic Evolution of Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infections over Two Time Periods at a Tertiary Care Hospital in South India: A Prospective Cohort Study

Infectious Diseases and Therapy

Introduction: The objective of this study was to examine the evolution of carbapenem-resistant Kl... more Introduction: The objective of this study was to examine the evolution of carbapenem-resistant Klebsiella pneumoniae (CRKp) infections and their impact at a tertiary care hospital in South India. Methods: A comparative analysis of clinical data from two prospective cohorts of patients with CRKp bacteremia (C1, 2014-2015; C2, 2021-2022) was carried out. Antimicrobial susceptibilities and whole genome sequencing (WGS) data of selected isolates were also analyzed. Results: A total of 181 patients were enrolled in the study, 56 from C1 and 125 from C2. CRKp bacteremia shifted from critically ill patients with neutropenia to others (ICU stay: C1, 73%; C2, 54%; p = 0.02). The overall mortality rate was 50% and the introduction of ceftazidime-avibactam did not change mortality Balaji Veeraraghavan and George M. Varghese are cocorresponding authors and contributed equally to this manuscript.

Research paper thumbnail of Persistent bacteremia predicts poor outcomes among neutropenic patients with carbapenem-resistant gram-negative bloodstream infections receiving appropriate therapy

Purpose Identifying persistent bacteremia early in patients with neutropenia may improve outcome.... more Purpose Identifying persistent bacteremia early in patients with neutropenia may improve outcome. This study evaluated the role of follow-up blood cultures (FUBC) positivity in predicting outcomes among patients with neutropenia and carbapenem-resistant gram-negative bloodstream infections (CRGNBSI). Methods This retrospective cohort study conducted between December 2017 and April 2022 included patients more than 15 years old with neutropenia and CRGNBSI, who survived for ≥ 48 hours, receiving appropriate antibiotic therapy and had FUBCs. Patients with polymicrobial bacteremia within 30 days were excluded. The primary outcome was 30-day mortality. Persistent bacteremia, septic shock, recovery from neutropenia, prolonged or profound neutropenia, requirement of intensive care and dialysis, and initiation of appropriate empirical therapy were also studied. Results The 30-day mortality rate was 47.7%. Persistent bacteremia was common in our patient cohort (43.8%). The median time for se...

Research paper thumbnail of In vitro activity of β-lactam-β-lactam enhancer combination, cefepime/zidebactam (WCK 5222, FEP/ZID) against multi-clonal, colistin-resistant Klebsiella pneumoniae

International Journal of Antimicrobial Agents, 2021

Research paper thumbnail of KPC-2 producing ST101 Klebsiella pneumoniae from bloodstream infection in India

Journal of Medical Microbiology, 2018

This study characterizes KPC-2 producing Klebsiella pneumoniae belonging to ST101. Whole genome s... more This study characterizes KPC-2 producing Klebsiella pneumoniae belonging to ST101. Whole genome sequencing using the Ion Torrent PGM platform with 400 bp chemistry was performed. bla KPC-2 was found on an IncFII K plasmid associated with ISKpn6 and ISKpn7 without Tn4401. This is the first report of KPC-2 K. pneumoniae from bacteremia in India. The isolate also coded for other resistance genes such as aadA1, aadA2, armA, aac(3)-Ild, aac(6¢)-Ild for aminoglycoside; bla SHV-11 , bla TEM-1B , bla OXA-9 , for b-lactams and aac(6¢)-Ild, oqxA, oqxB, qnrB1 for fluoroquinolones. It belonged to the K17 capsular type. India is endemic to New Delhi metallo-b-lactamase and OXA48-like carbapenemases and K. pneumoniae carbapenemase (KPC) is seldom reported. With high rates of carbapenem resistance, emergence of KPC in India will challenge patient management. The isolate was susceptible to colistin. The patient had a fatal outcome. Klebsiella pneumoniae is a common pathogen causing invasive infections such as urinary tract infection, pneumonia, liver abscess and sepsis. K. pneumoniae carbapenemases (KPCs) producing K. pneumoniae infections are often associated with high mortality rates of 50 to 66 % [1, 2]. The high rates of carbapenem and colistin resistance, along with virulence factors, make it difficult to eliminate. Carbapenem resistance in K. pneumoniae is chiefly due to carbapenemase enzymes such as New Delhi metallo-b-lactamase (NDM), KPC, OXA48-like carbapenemases and Verona integron-encoded metallo-b-lactamase (VIM). KPC is the common enzyme causing carbapenem resistance in USA, China, South America and Europe but is rarely reported from India, which is endemic for NDM and OXA48-like carbapenemases [3, 4]. VIM is rarely reported in India among K. pneumoniae isolates [5, 6]. To date, 24 KPC variants have been described (www.lahey. org/Studies/other.asp). bla KPC-2 has been reported among diverse plasmid types, such as IncX3, IncFII K and IncFIA, and has a diverse genetic background [7]. bla KPC has been reportedly associated with several genetic elements such as transposon Tn4401 and its eight variants [8-10]; other non-Tn4401 elements (NTE KPC) have also been reported

Research paper thumbnail of Genomic insights into multi-drug and extensively drug resistant Klebsiella pneumoniae from India

International Journal of Infectious Diseases, 2020

Research paper thumbnail of Extremely High Mortality Rates in Patients with Carbapenem-resistant, Hypermucoviscous Klebsiella pneumoniae Blood Stream Infections

The Journal of the Association of Physicians of India, 2018

Background Infections caused by carbapenem resistant K. pneumoniae are increasing and associated ... more Background Infections caused by carbapenem resistant K. pneumoniae are increasing and associated with high mortality rates. There are increasing reports of hypermucoviscous/ hypervirulent K. pneumoniae isolated from various sources. However, there is limited data on the prevalence of hypermucoviscous strains among carbapenem-resistant K. pneumoniae from invasive infections in India and its association with mortality. rmpA, rmpA2 and magA genes are associated with these hypervirulent strains. In this study, we investigate the prevalence of hypermucoviscous strains amongst carbapenem resistant K. pneumoniae isolated from blood culture. Association of mortality rate with meropenem minimum inhibitory concentration and hypermucoviscous strains are determined. Methods 86 non-repetitive carbapenem resistant K. pneumoniae isolated from bacteremia underwent E-test for meropenem minimum inhibitory concentration (MIC) determination and PCR for detection of carbapenamase genes. String test, PCR...

Research paper thumbnail of Distinctive Mobile Genetic Elements Observed in the Clonal Expansion of Carbapenem-Resistant Klebsiella pneumoniae in India

Microbial Drug Resistance, 2021

Background: Klebsiella pneumoniae (Kp), a common multidrug-resistant pathogen, causes a wide spec... more Background: Klebsiella pneumoniae (Kp), a common multidrug-resistant pathogen, causes a wide spectrum of nosocomial infections with high rates of morbidity and mortality. The emergence of pan drug-resistant international high-risk clones such as ST258, ST14, ST15, ST147, and ST101 is a global concern. This study was performed to investigate the carbapenemases, the plasmid profile, and the clonal relationship among Indian K. pneumoniae. Materials and Methods: A total of 290 K. pneumoniae isolates from seven centers in India were characterized to determine sequence types (STs) and carbapenemases. A subset of isolates was subjected to whole genome sequencing and hybrid genome assembly to obtain the complete genome. Plasmids carrying carbapenemases were characterized to determine the dissemination of carbapenem-resistant (CR) K. pneumoniae. Results: From this study, 75 different STs were observed with ST231 being predominant. About 79% of the analyzed isolates were CR with 59% (n = 136) producing OXA48-like carbapenemases. While ST231 was the predominant clone among the OXA48-like producers; NDM producers and NDM+OXA48-like producers were mostly associated with ST14. Interestingly, 61% (n = 138) of the total CR K. pneumoniae were colistin resistant, belonging to 22 different STs. Plasmid profiling shows that blaOXA48-like was exclusively carried by ColKP3, whereas blaNDM was associated with IncFII-like plasmids. Conclusion: The highly mosaic genome of K. pneumoniae coupled with the diverse ecological niches in India makes it a hotspot for antimicrobial resistance, leading to increased morbidity and mortality. Extensive molecular surveillance of the clonal spread of K. pneumoniae could help in understanding AMR dynamics and thus rework therapeutic management.

Research paper thumbnail of Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096 Klebsiella pneumoniae in India: The rise of a new superbug?

ABSTRACTHypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp... more ABSTRACTHypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed to characterise nine novel MDR hvKp isolates harbouring mosaic plasmids simultaneously carrying antimicrobial resistance (AMR) and virulence genes. Nine HvKp isolates obtained from hospitalised patients in southern India were characterized for antimicrobial susceptibility and hypervirulence phenotypes. All nine hvKp isolates were subjected to whole genome sequencing (WGS) using Ilumina HiSeq2500 and a subset of four were sequenced using Oxford Nanopore MinION. Among the nine isolates, seven were carbapenem-resistant, two of which carried blaNDM-5 on an IncFII plasmid and five carried blaOXA-232 on a ColKP3 plasmid. The virulence determinants were encoded in a mosaic plasmid (∼320 Kbp) that formed as a result of its insertion in a IncFIB-IncHI1B plasmid co-integrate. The mosaic pl...

Research paper thumbnail of Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens

Indian Journal of Medical Microbiology, 2019

The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, wh... more The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.

Research paper thumbnail of In vitro activity of β-lactam-β-lactam enhancer combination, cefepime/zidebactam (WCK 5222, FEP/ZID) against multi-clonal, colistin-resistant Klebsiella pneumoniae

International Journal of Antimicrobial Agents, Sep 1, 2021

Research paper thumbnail of Emergence of Multidrug Resistant Hypervirulent ST23 Klebsiella pneumoniae: Multidrug Resistant Plasmid Acquisition Drives Evolution

Frontiers in Cellular and Infection Microbiology, Nov 20, 2020

Background: In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MD... more Background: In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used the complete genome sequence of two MDR hvKp isolates belonging to ST23 to characterize the phylogenetic background and plasmid diversity. Methods: Two hvKp isolates from patients with bacteremia were sequenced using Ion Torrent PGM and Oxford Nanopore MinION platforms and assembled by hybrid genome assembly approach. Comparative genomics approaches were used to investigate the population structure, evolution, virulence, and antimicrobial resistance of MDR hvKp strains. Results: The study isolates exhibited typical features of hvKp phenotypes associated with ST23. The convergence of multidrug resistance and hypervirulence were attributed by the presence of multiple plasmids including a 216 kb virulence plasmid and MDR plasmids belonging to IncA/C 2 , IncFIB, IncX3, and ColKP3 groups. The insertion of catA1 gene into virulence plasmid was observed along with genetic factors such as aerobactin, salmochelin, and rmpA2 that confer hvKp's hypervirulent phenotype. The core genome single nucleotide polymorphism (SNP) phylogenetic analyses of the isolates showed the evolution of ST23 hvKp was predominantly driven by ICEKp acquisitions. Conclusion: To the best of our knowledge, this is the first report of MDR hvKp isolates of ST23 with insertion of catA1 gene into the virulence plasmid which presents the possibility of hotspot integration sites on the plasmids to aid acquisition of AMR genes. ST23 is no longer confined to susceptible strains of hvKp. Our findings emphasize the need for more studies on recombinant events, plasmid transmission dynamics and evolutionary process involving hvKp.

Research paper thumbnail of Genomic insights into multi-drug and extensively drug resistant Klebsiella pneumoniae from India

International Journal of Infectious Diseases, Dec 1, 2020

Research paper thumbnail of Bad Bug, No Test: Tigecycline Susceptibility Testing Challenges and Way Forward

Indian Journal of Medical Microbiology, 2019

There is a drastic increase in the incidence of extensively drug-resistant Gram-negative bacteria... more There is a drastic increase in the incidence of extensively drug-resistant Gram-negative bacteria in the recent times, especially in India. Klebsiella pneumoniae and Acinetobacter baumannii are the two most common pathogens with high drug-resistant rates of up to 40% and 70% carbapenem resistance, respectively. [1] Very few agents are available for the management of these drug-resistant infections. Tigecycline and colistin are the drugs of last resort for treatment as single agents/in combination with other antibiotics. However, both these agents have shortcomings in terms of susceptibility testing, which significantly impact on its right use. Tigecycline is approved for the treatment of Gram-positive and Gram-negative bacteria causing intra-abdominal infections and skin and soft tissue infections. [2] However, it is used off-label for the treatment of other infections such as septicaemia. Tigecycline is a reserve antibiotic increasingly used for the treatment of multidrug-resistant bacteria, especially Klebsiella pneumoniae and Acinetobacter baumannii. At present, there are concerns regarding the testing and interpretation of tigecycline susceptibility to bugs such as K. pneumoniae and A. baumannii, which limit clinicians in appropriate usage. Use of appropriate method for testing such as broth microdilution is essential. In addition, tigecycline susceptibility testing is a challenge due to inconsistent results from various antimicrobial susceptibility testing automated platforms. There is a great need to define a suitable methodology along with interpretive criteria, especially for K. pneumoniae and A. baumannii. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Food and Drug Administration (FDA) breakpoints show wide variation and are defined for different set of organisms. Non-species-related pharmacokinetic/pharmacodynamic (PK/ PD) breakpoints defined by the EUCAST can be used for organisms such as K. pneumoniae and A. baumannii.

Research paper thumbnail of Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096 <i>Klebsiella pneumoniae</i> in India: The rise of a new superbug?

Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also... more Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed to characterise nine novel MDR hvKp isolates harbouring mosaic plasmids simultaneously carrying antimicrobial resistance (AMR) and virulence genes. Nine HvKp isolates obtained from hospitalised patients in southern India were characterized for antimicrobial susceptibility and hypervirulence phenotypes. All nine hvKp isolates were subjected to whole genome sequencing (WGS) using Ilumina HiSeq2500 and a subset of four were sequenced using Oxford Nanopore MinION. Among the nine isolates, seven were carbapenem-resistant, two of which carried bla NDM-5 on an IncFII plasmid and five carried bla OXA-232 on a ColKP3 plasmid. The virulence determinants were encoded in a mosaic plasmid (~320 Kbp) that formed as a result of its insertion in a IncFIB-IncHI1B plasmid co-integrate. The mosaic plasmid carried AMR genes (aadA2, armA, blaOXA-1, msrE, mphE, sul1 and dfrA14) in addition to rmpA2, iutA and iucABCD virulence genes. Interestingly the mosaic plasmid carried its own type IV-A3 CRISPR-cas system that is likely able to target the acquisition of IncF plasmid with the help of a traL spacer. The convergence of virulence and AMR is the biggest threat among invasive K. pneumoniae infections. However, increasing reports of the presence of mosaic plasmid carrying both AMR and virulence genes suggests MDR-hvKp isolates are no longer confined to selected clones and the containment of such isolates is very challenging. IMPORTANCE Klebsiella pneumoniae is an opportunistic pathogen that commonly associated with hospital-acquired infections in the urinary tract, respiratory tract, lung, wound sites. The organism has gained notoriety by acquiring additional genetic traits to become either hypervirulent (HV) phenotype or multidrug resistant (MDR) phenotype. Though the infections by both these phenotypes were very challenging to treat, the MDR K. pneumonia (MDR-Kp) were remained in the hospital settings while HV K. pneumonia (hvKp) strains were mostly originated from the community settings. In a recent turn of events, the evolution of MDR-Kp and hvKp has converged as both clones found to carry both MDR plasmids and virulence plasmid. These convergent strains are challenging to treat and is associated with higher mortality rate. As the recent hvKp isolates harbour mosaic plasmid encoding both AMR

Research paper thumbnail of First Report of Whole-Genome Sequence of Colistin-Resistant <i>Klebsiella quasipneumoniae</i> subsp. <i>similipneumoniae</i> Producing KPC-9 in India

Microbial Drug Resistance, May 1, 2019

Aim: Klebsiella pneumoniae carbapenemase (KPC) is a class A carbapenemase endemic in the United S... more Aim: Klebsiella pneumoniae carbapenemase (KPC) is a class A carbapenemase endemic in the United States, China, South America, and Europe but is rarely reported from India. A single report of KPC-9 from K. pneumoniae in Israel has been published. K. pneumoniae has been classified into three phylogenetic groups: group 1 consists of K. pneumoniae and its subspecies, group 2 consists of Klebsiella quasipneumoniae and its subspecies, and group 3 consists of Klebsiella variicola. This is the first report of whole-genome sequencing of colistin-resistant K. quasipneumoniae subsp. similipneumoniae harboring blaKPC-9 gene. Results: The isolate was obtained from the culture of a respiratory catheter tip from a 41-year-old woman with traumatic brain injury. Whole-genome sequencing showed the presence of blaOKP-B-3 gene and hence it was identified as K. quasipneumoniae subsp. similipneumoniae. The isolate was resistant to all antimicrobials except tigecycline. Colistin resistance was chromosomally mediated; mcr-1 to mcr-5 genes and their variants were not identified. The isolate belonged to the novel clonal type ST2957. Conclusion: The isolation of KPC-9 from India, a nonendemic region, and in an isolate of K. quasipneumoniae highlights the importance of accurate identification of Klebsiella species and determination of mechanism of resistance. The novel sequence type obtained indicates evolution of the organism and acquisition of plasmid-mediated resistance. The occurrence of KPC in India is a potential public health threat.

Research paper thumbnail of Identification of plasmids by PCR based replicon typing in bacteremic Klebsiella pneumoniae

Microbial Pathogenesis, Nov 1, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Research paper thumbnail of Emergence of ST147 Klebsiella pneumoniae carrying bla on IncA/C2 with ompK35 and ompK36 mutations in India

Journal of Infection and Public Health, Sep 1, 2019

India is known to be endemic to NDM carbapenemases. However, NDM-7 among Klebsiella pneumoniae ha... more India is known to be endemic to NDM carbapenemases. However, NDM-7 among Klebsiella pneumoniae has not been described from India. Apart from carbapenemases, ompK35 and ompK36 also contribute to carbapenem resistance in K. pneumoniae. This study describes molecular mechanisms of antimicrobial resistance in an isolate from bacteraemia investigated through whole genome sequencing. bla NDM-7 was found on IncA/C2 plasmid which also carried sul-1, aadA2, rmtC, bla CMY-6 and ARR-2. ompK35 had mutations and changes from 39th amino acid. ompK36 was truncated to 248 amino acids. The isolate belonged to ST147. The patient was a known case systemic lupus erythematosus (SLE) and blood culture grew carbapenem resistant K. pneumoniae. Meropenem, colistin and tiecoplanin were administered and the patient was discharged on improvement. Emergence of new resistance variants and porin mutations among clones such as ST147 which has been prevalent has potential for rapid spread and thus challenges infection control.

Research paper thumbnail of Molecular characterization of colistin-resistant Klebsiella pneumoniae & its clonal relationship among Indian isolates

Indian Journal of Medical Research, 2019

Background & objectives: Klebsiella pneumoniae (KP), a common cause of invasive infections, i... more 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 21st 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.

Research paper thumbnail of Hybrid Plasmids Encoding Antimicrobial Resistance and Virulence Traits Among Hypervirulent Klebsiella pneumoniae ST2096 in India

Frontiers in Cellular and Infection Microbiology

BackgroundHypervirulent variants ofKlebsiella pneumoniae(HvKp) were typically associated with a b... more BackgroundHypervirulent variants ofKlebsiella pneumoniae(HvKp) were typically associated with a broadly antimicrobial susceptible clone of sequence type (ST) 23 at the time of its emergence. Concerningly, HvKp is now also emerging within multidrug-resistant (MDR) clones, including ST11, ST15, and ST147. MDR-HvKp either carry both the virulence and resistance plasmids or carry a large hybrid plasmid coding for both virulence and resistance determinants. Here, we aimed to genetically characterize a collection of MDR-HvKp ST2096 isolates haboring hybrid plasmids carrying both antimicrobial resistance (AMR) and virulence genes.MethodsNineK. pneumoniaeST2096 isolated over 1 year from the blood sample of hospitalized patients in southern India that were MDR and suspected to be HvKp were selected. All nine isolates were subjected to short-read whole-genome sequencing; a subset (n = 4) was additionally subjected to long-read sequencing to obtain complete genomes for characterization. Mucovi...

Research paper thumbnail of Correlation of carbapenem resistance and hypermucoviscosity in K.pneumoniae isolated from blood culture at a tertiary hospital in South India

International Journal of Infectious Diseases, 2016

efflux-pump gene expressions (marA, mdfA) were also checked for the MDR isolates. Results: Out of... more efflux-pump gene expressions (marA, mdfA) were also checked for the MDR isolates. Results: Out of 453 samples screened for E. coli, 386 (85.2%) isolates was recovered, while 47 (7.03%) Salmonella was isolated from 668 samples examined. Above 6 percent E. coli showed resistance to all the tested antibiotics. Over 80 percent Salmonella were resistant to amikacin, cefazolin and tobramycin and other remaining exhibited high frequency of resistance against cefuroxime (74.5%) and gentamicin (68.1%). Overall marA gene was the most common type with 15 percent harboring the gene. Above 10.8 percent isolates possessed sul1, sul2, tetA, strA genes and above 5 percent carried tetB, aadA, armA, bla TEM and bla CTX-M , however, bla SHV gene, armB and rmtC were not recovered. Plasmid mediated quinolone resistant gene positive strains totaled to 4.4 (qnrB) and 2.07 (qnrS) percent while qnrA was not detected. Species and region-wise distributions were variable. Resistant traits were transferable and the resistant isolates had shown ≥2 fold increase in the expression level of marA. ' Conclusion: Emergence of MDR in E. coli or Salmonella among the animal populations of NE India was evident from the study revealing above 85 percent MDR isolates. These results emphasize the urgent need for surveillance of antibiotic resistance incorporating rational and regulated use of antibiotics in Livestock farming.

Research paper thumbnail of Clinical and Genomic Evolution of Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infections over Two Time Periods at a Tertiary Care Hospital in South India: A Prospective Cohort Study

Infectious Diseases and Therapy

Introduction: The objective of this study was to examine the evolution of carbapenem-resistant Kl... more Introduction: The objective of this study was to examine the evolution of carbapenem-resistant Klebsiella pneumoniae (CRKp) infections and their impact at a tertiary care hospital in South India. Methods: A comparative analysis of clinical data from two prospective cohorts of patients with CRKp bacteremia (C1, 2014-2015; C2, 2021-2022) was carried out. Antimicrobial susceptibilities and whole genome sequencing (WGS) data of selected isolates were also analyzed. Results: A total of 181 patients were enrolled in the study, 56 from C1 and 125 from C2. CRKp bacteremia shifted from critically ill patients with neutropenia to others (ICU stay: C1, 73%; C2, 54%; p = 0.02). The overall mortality rate was 50% and the introduction of ceftazidime-avibactam did not change mortality Balaji Veeraraghavan and George M. Varghese are cocorresponding authors and contributed equally to this manuscript.

Research paper thumbnail of Persistent bacteremia predicts poor outcomes among neutropenic patients with carbapenem-resistant gram-negative bloodstream infections receiving appropriate therapy

Purpose Identifying persistent bacteremia early in patients with neutropenia may improve outcome.... more Purpose Identifying persistent bacteremia early in patients with neutropenia may improve outcome. This study evaluated the role of follow-up blood cultures (FUBC) positivity in predicting outcomes among patients with neutropenia and carbapenem-resistant gram-negative bloodstream infections (CRGNBSI). Methods This retrospective cohort study conducted between December 2017 and April 2022 included patients more than 15 years old with neutropenia and CRGNBSI, who survived for ≥ 48 hours, receiving appropriate antibiotic therapy and had FUBCs. Patients with polymicrobial bacteremia within 30 days were excluded. The primary outcome was 30-day mortality. Persistent bacteremia, septic shock, recovery from neutropenia, prolonged or profound neutropenia, requirement of intensive care and dialysis, and initiation of appropriate empirical therapy were also studied. Results The 30-day mortality rate was 47.7%. Persistent bacteremia was common in our patient cohort (43.8%). The median time for se...

Research paper thumbnail of In vitro activity of β-lactam-β-lactam enhancer combination, cefepime/zidebactam (WCK 5222, FEP/ZID) against multi-clonal, colistin-resistant Klebsiella pneumoniae

International Journal of Antimicrobial Agents, 2021

Research paper thumbnail of KPC-2 producing ST101 Klebsiella pneumoniae from bloodstream infection in India

Journal of Medical Microbiology, 2018

This study characterizes KPC-2 producing Klebsiella pneumoniae belonging to ST101. Whole genome s... more This study characterizes KPC-2 producing Klebsiella pneumoniae belonging to ST101. Whole genome sequencing using the Ion Torrent PGM platform with 400 bp chemistry was performed. bla KPC-2 was found on an IncFII K plasmid associated with ISKpn6 and ISKpn7 without Tn4401. This is the first report of KPC-2 K. pneumoniae from bacteremia in India. The isolate also coded for other resistance genes such as aadA1, aadA2, armA, aac(3)-Ild, aac(6¢)-Ild for aminoglycoside; bla SHV-11 , bla TEM-1B , bla OXA-9 , for b-lactams and aac(6¢)-Ild, oqxA, oqxB, qnrB1 for fluoroquinolones. It belonged to the K17 capsular type. India is endemic to New Delhi metallo-b-lactamase and OXA48-like carbapenemases and K. pneumoniae carbapenemase (KPC) is seldom reported. With high rates of carbapenem resistance, emergence of KPC in India will challenge patient management. The isolate was susceptible to colistin. The patient had a fatal outcome. Klebsiella pneumoniae is a common pathogen causing invasive infections such as urinary tract infection, pneumonia, liver abscess and sepsis. K. pneumoniae carbapenemases (KPCs) producing K. pneumoniae infections are often associated with high mortality rates of 50 to 66 % [1, 2]. The high rates of carbapenem and colistin resistance, along with virulence factors, make it difficult to eliminate. Carbapenem resistance in K. pneumoniae is chiefly due to carbapenemase enzymes such as New Delhi metallo-b-lactamase (NDM), KPC, OXA48-like carbapenemases and Verona integron-encoded metallo-b-lactamase (VIM). KPC is the common enzyme causing carbapenem resistance in USA, China, South America and Europe but is rarely reported from India, which is endemic for NDM and OXA48-like carbapenemases [3, 4]. VIM is rarely reported in India among K. pneumoniae isolates [5, 6]. To date, 24 KPC variants have been described (www.lahey. org/Studies/other.asp). bla KPC-2 has been reported among diverse plasmid types, such as IncX3, IncFII K and IncFIA, and has a diverse genetic background [7]. bla KPC has been reportedly associated with several genetic elements such as transposon Tn4401 and its eight variants [8-10]; other non-Tn4401 elements (NTE KPC) have also been reported

Research paper thumbnail of Genomic insights into multi-drug and extensively drug resistant Klebsiella pneumoniae from India

International Journal of Infectious Diseases, 2020

Research paper thumbnail of Extremely High Mortality Rates in Patients with Carbapenem-resistant, Hypermucoviscous Klebsiella pneumoniae Blood Stream Infections

The Journal of the Association of Physicians of India, 2018

Background Infections caused by carbapenem resistant K. pneumoniae are increasing and associated ... more Background Infections caused by carbapenem resistant K. pneumoniae are increasing and associated with high mortality rates. There are increasing reports of hypermucoviscous/ hypervirulent K. pneumoniae isolated from various sources. However, there is limited data on the prevalence of hypermucoviscous strains among carbapenem-resistant K. pneumoniae from invasive infections in India and its association with mortality. rmpA, rmpA2 and magA genes are associated with these hypervirulent strains. In this study, we investigate the prevalence of hypermucoviscous strains amongst carbapenem resistant K. pneumoniae isolated from blood culture. Association of mortality rate with meropenem minimum inhibitory concentration and hypermucoviscous strains are determined. Methods 86 non-repetitive carbapenem resistant K. pneumoniae isolated from bacteremia underwent E-test for meropenem minimum inhibitory concentration (MIC) determination and PCR for detection of carbapenamase genes. String test, PCR...

Research paper thumbnail of Distinctive Mobile Genetic Elements Observed in the Clonal Expansion of Carbapenem-Resistant Klebsiella pneumoniae in India

Microbial Drug Resistance, 2021

Background: Klebsiella pneumoniae (Kp), a common multidrug-resistant pathogen, causes a wide spec... more Background: Klebsiella pneumoniae (Kp), a common multidrug-resistant pathogen, causes a wide spectrum of nosocomial infections with high rates of morbidity and mortality. The emergence of pan drug-resistant international high-risk clones such as ST258, ST14, ST15, ST147, and ST101 is a global concern. This study was performed to investigate the carbapenemases, the plasmid profile, and the clonal relationship among Indian K. pneumoniae. Materials and Methods: A total of 290 K. pneumoniae isolates from seven centers in India were characterized to determine sequence types (STs) and carbapenemases. A subset of isolates was subjected to whole genome sequencing and hybrid genome assembly to obtain the complete genome. Plasmids carrying carbapenemases were characterized to determine the dissemination of carbapenem-resistant (CR) K. pneumoniae. Results: From this study, 75 different STs were observed with ST231 being predominant. About 79% of the analyzed isolates were CR with 59% (n = 136) producing OXA48-like carbapenemases. While ST231 was the predominant clone among the OXA48-like producers; NDM producers and NDM+OXA48-like producers were mostly associated with ST14. Interestingly, 61% (n = 138) of the total CR K. pneumoniae were colistin resistant, belonging to 22 different STs. Plasmid profiling shows that blaOXA48-like was exclusively carried by ColKP3, whereas blaNDM was associated with IncFII-like plasmids. Conclusion: The highly mosaic genome of K. pneumoniae coupled with the diverse ecological niches in India makes it a hotspot for antimicrobial resistance, leading to increased morbidity and mortality. Extensive molecular surveillance of the clonal spread of K. pneumoniae could help in understanding AMR dynamics and thus rework therapeutic management.

Research paper thumbnail of Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096 Klebsiella pneumoniae in India: The rise of a new superbug?

ABSTRACTHypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp... more ABSTRACTHypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed to characterise nine novel MDR hvKp isolates harbouring mosaic plasmids simultaneously carrying antimicrobial resistance (AMR) and virulence genes. Nine HvKp isolates obtained from hospitalised patients in southern India were characterized for antimicrobial susceptibility and hypervirulence phenotypes. All nine hvKp isolates were subjected to whole genome sequencing (WGS) using Ilumina HiSeq2500 and a subset of four were sequenced using Oxford Nanopore MinION. Among the nine isolates, seven were carbapenem-resistant, two of which carried blaNDM-5 on an IncFII plasmid and five carried blaOXA-232 on a ColKP3 plasmid. The virulence determinants were encoded in a mosaic plasmid (∼320 Kbp) that formed as a result of its insertion in a IncFIB-IncHI1B plasmid co-integrate. The mosaic pl...

Research paper thumbnail of Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens

Indian Journal of Medical Microbiology, 2019

The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, wh... more The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.