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Objectives: Elizabethkingia spp. are Gram-negative, glucose-non-fermenting bacilli that are ubiquitous in natural environments such as soil, plant and water sources. Besides environmental sources, the bacterium can be found in hospital environments, particularly medical equipment and reagents. Here we report the draft genome sequence of an Elizabethkingia anophelis isolate from a blood culture., Methods: Genomic DNA of E. anophelis strain BP8467 was sequenced on an Ion Torrent PGM platform and the reads were assembled de novo using SPAdes v.5.0.0. The draft genome was annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) v.4.9. Genetic determinants of antimicrobial resistance as well as virulence factors were identified using computational tools., Results: The assembled draft genome is 3859105bp in length with a G+C content of 35.62% distributed in 30 contigs. Presence of the bla BlaB and bla GOB-4 genes associated with resistance to carbapenems was identified. In addition, genes conferring resistance to other β-lactams (bla CME-1 ), aminoglycosides [ant(6)-I] and chloramphenicol (catB) were also detected. Antimicrobial susceptibility testing showed that the isolate was susceptible to levofloxacin, trimethoprim/sulfamethoxazole, tetracycline and rifampicin., Conclusion: The presence of a multidrug-resistant isolate harbouring diverse antimicrobial resistance genes along with numerous virulence factors suggests the risk associated with Elizabethkingia spp. infections. This genome analysis provides insights into the antimicrobial resistance and pathogenicity mechanisms of multidrug-resistant E. anophelis that can help in the management of Elizabethkingia spp. infections in the future., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: With the increasing incidence of multidrug-resistant (MDR) organisms and high mortality rates associated with these infections, we describe the spectrum of the major drug-resistant pathogens identified in fecal surveillance, and re-visit the use of fecal surveillance in predicting infection with these organisms post-allogeneic stem cell transplant., Methods: Data from allogeneic stem cell transplant recipients with common drug-resistant strains of bacteria in fecal surveillance (Escherichia coli, Klebsiella spp., and Enterococcus spp.) were compared with recipients who did not have the same in fecal surveillance cultures. Baseline characteristics and post-transplant outcomes including similar drug resistance in blood cultures, severe sepsis, and 100-day transplant-related mortality were compared. Multivariate analysis using logistic regression model was used to determine independent predictors of outcome., Results: In 232 transplants, the prevalence of common drug-resistant isolates in fecal surveillance cultures was 57.7% (134 out of 232 patients-with a single isolate in 115 and ≥2 isolates in the remaining 19 patients. A total of 164 drug-resistant isolates were obtained from 134 patients. Of the 164 isolates, 133 (81%) were positive for ESBL screening, 19 (11.5%) for carbapenem-resistant organisms (CRO) screening, 12 (7.3%) for VRE screening. Patients who had common drug-resistant pathogens detected in fecal surveillance have significantly higher subsequent blood culture positivity with drug resistance, as well as higher 100-day mortality. Factors influencing 100-day mortality included patient's age (P = .001), drug resistance positivity in blood (P < .001), drug resistance in fecal surveillance (P = .011), use of an alternate donor (other than fully matched sibling) (P < .001), GVHD grade 3-4 (P < .001), and severe sepsis (P < .001). On multivariate analysis, only use of an alternate donor (0.024), severe sepsis (P < .001), and grade 3-4 GVHD (P < .001) retained significance in predicting 100-day mortality., Conclusion: Organisms resistant to 3rd generation cephalosporins are frequently seen on fecal surveillance in the pre-transplant setting and are associated with a higher incidence of drug-resistant organisms in subsequent blood cultures (not limited to the same drug resistance pattern as seen in fecal surveillance). Drug-resistant organisms in fecal surveillance are associated with poorer outcomes following allogeneic stem cell transplant and may be used as a guide to identify patients at risk of subsequently developing a drug-resistant organism in blood., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Background: Multidrug-resistant Gram-negative neonatal sepsis is associated with high mortality and morbidity. Mucosal colonization with these organisms in hospitals may predispose neonates to septicemia., Aims: The aim of the study was to determine the prevalence and pattern of colonization of neonatal preterm gut with carbapenem-resistant Enterobacteriaceae and identify risk factors associated with colonization., Settings and Design: The study was a prospective observational study done in a Level 3 neonatal unit of a tertiary care hospital., Methods: Stool samples from preterm babies were collected soon after birth and at 1 and 3 weeks of age after consent. Maternal stool sample was collected within 48 h after the delivery. Predetermined antenatal, neonatal, and environmental risk factors were recorded. Isolation and identification of organisms was done in a standardized manner; antibiotic susceptibility was done by the Kirby-Bauer method and results interpreted according to the Clinical and Laboratory Standards Institute guidelines., Results: Seventy-one percent of the babies were colonized by Gram-negative bacteria (GNB) at birth, and 100% were colonized by the end of the 1 st week. The organisms commonly isolated were Escherichia coli , Klebsiella , NFGNB (Nonfermenting Gram-Negative Bacilli), Pseudomonas , and Enterobacter . Sixty-eight percent of the babies were colonized with extended-spectrum beta-lactamase-producing organisms, and 5% of the babies were colonized with carbapenem-resistant organisms (CROs). In the babies who developed culture-positive sepsis, 21% had concordance of strains in the gut and blood. There was no association between maternal and neonatal colonization., Conclusions: The results show that neonatal gut is colonized by GNB from birth onward. However, the rate of colonization with CRO is low. An association was also observed between colonization and late-onset sepsis., Competing Interests: There are no conflicts of interest., (Copyright: © 2020 Journal of Global Infectious Diseases.)

Context: Tuberculosis (TB) and diabetes mellitus (DM) are converging epidemics, each worsening the morbidity of the other. A study of the prevalence of DM in TB patients assumes great importance., Aims: The study aims to evaluate the association between DM and TB over a 10-year period in a tertiary care hospital., Settings and Design: A retrospective observational study in a southern Indian tertiary care teaching hospital was conducted., Materials and Methods: All patients with TB diagnosed and treated during the 10-year study period were identified from the hospital database. All relevant clinical, microbiological, and laboratory results pertaining to diagnosis of DM were collected. The diagnosis of TB and DM was made as per the standard criteria., Statistical Analysis: Categorical variables were analyzed using Chi-square test while continuous variables using independent sample t-test., Results: From 2001 to 2012, we studied 1979 TB patients among whom data on DM were available. The prevalence of DM was 29%, 21%, and 14%, in smear positive, smear negative and extrapulmonary TB respectively (overall 24%). Diabetics were more likely to be men (77.3% vs. 61%;P = 0.001); >40 years of age (81.7% vs. 38.9%;P < 0.001); heavier (59.96 vs. 50.37;P = 0.004); tobacco smokers (16.1% vs. 8.1%;P < 0.001); and alcohol consumers (6.8% vs. 4%;P = 0.02). They were less likely to be HIV coinfected (1.8% vs. 6.1%;P < 0.001). HIV coinfection was seen in 5% of patients and was substantially higher in extrapulmonary TB group (19.4%). Multidrug-resistant TB was lower in DM (11.7%) compared to non-DM (15.9%) (P = 0.02). Overall, 48% of the DM patients were diagnosed at the time of TB diagnosis. Over 10 years, no obvious changes in the trend were evident., Conclusions: Over a 10-year study period, 24% of the TB patients were diabetic, nearly half were detected at the time of TB diagnosis. There may be a good case for screening all TB patients for DM., Competing Interests: None

In India and China, indigenous drug manufacturers market arbitrarily combined parenteral β-lactam and β-lactamase inhibitors (BL-BLIs). In these fixed-dose combinations, sulbactam or tazobactam is indiscriminately combined with parenteral cephalosporins, with BLI doses kept in ratios similar to those for the approved BL-BLIs. Such combinations have been introduced into clinical practice without mandatory drug development studies involving pharmacokinetic/pharmacodynamic, safety, and efficacy assessments being undertaken. Such unorthodox combinations compromise clinical outcomes and also potentially contribute to resistance development., (Copyright © 2020 American Society for Microbiology.)

Introduction: Streptococcus pneumoniae is one of the frequently isolated organisms and an important aetiological agent of invasive bacterial diseases (IBD) like pneumonia, meningitis and sepsis. As a measure to control the burden of IBD, the Government of India introduced Pneumoccocal Conjugate Vaccine-13 (PCV-13) in the Universal Immunization Program in high burden districts of five states in a phased manner from 2017 onwards. It is essential to understand the trend of circulating pneumococcal serotypes associated with IBD in the prevaccination and postvaccination scenarios to decide on the expansion of vaccination programmes and PCV reformulation. This manuscript describes the protocol for hospital-based sentinel surveillance for S. pneumoniae and other organisms causing IBD across various geographical regions in India., Methods and Analysis: Hospital-based surveillance is established in selected hospitals to recruit children aged 1-59 months with symptoms of pneumonia and other IBD. Diagnostic criteria were adapted from standard WHO case definitions. Case Report Forms (CRFs) are used to collect data from the enrolled children. Blood, cerebrospinal fluid (CSF) and other normally sterile body fluids are collected and subjected to microscopy, cytology, latex agglutination, biochemistry, bacteriological culture and real-time PCR as applicable. Pneumococcal isolates are serotyped and tested for assessing antimicrobial resistance patterns. Data will be analysed by simple descriptive statistics to estimate the proportion of pneumonia and other IBD due to S. pneumoniae , Hemophilus influenzae type b and Neisseria meningitidis . Prevalence of bacterial infection, circulating pneumococcal serotypes, antibiotic resistance patterns, serotype variability across seasons and regions will be described in terms of percentage with 95% confidence interval., Ethics and Dissemination: The institutional review boards of the coordinating centre, all sentinel sites, regional and national reference laboratories approved the project. The results will be published in peer-reviewed journals and shared with stakeholders for deciding on revising vaccination strategy appropriately., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and subsequent containment procedures have impacted the world as never seen before. Therefore, there is considerable curiosity about the genome evolution related to the origin, transmission and vaccine impact of this virus. We have analysed genome sequences of SARS-CoV-2 isolated from Indian patients to gain an in-depth understanding of genomic evolution and transmission in India. Phylogenetic analysis and mutation profiling revealed major lineages being evolved by characteristic mutations. As the mutation frequency in spike protein is comparatively lesser, the candidate vaccines expected to have wide coverage worldwide including India., Competing Interests: None

Aim: To evaluate the antibacterial activity of fosfomycin-meropenem and fosfomycin-colistin combinations against carbapenem-resistant Klebsiella pneumoniae (CR-Kp)., Methods: A total of 50 CR-Kp isolates recovered from blood cultures were included in this study. All the CR-Kp isolates were screened for the presence of carbapenem resistant genes bla IMP . bla VIM . bla NDM . bla OXA-48 like, bla KPC . bla GES .#x00A0;and bla SPM . Combination testing of fosfomycin-meropenem and fosfomycin-colistin were performed using time-kill assay., Results: Fosfomycin-meropenem combination showed synergy in 20% of the tested CR-Kp isolates. While, fosfomycin-colistin exhibited synergy against 16% of the isolates. A total of 68% (n = 34) of CR-Kp isolates were characterised as OXA-48-like producers and 22% (n = 11) as NDM producers. Synergistic activity of these combinations was observed against OXA-48, NDM and NDM + OXA-48 co-producers., Conclusion: Considerable synergistic antibacterial activity of fosfomycin-meropenem and fosfomycin-colistin was not observed against CR-Kp isolates. Therefore, these combinations may not be promising for infections associated with CR-Kp., Competing Interests: Financial & competing interests disclosure The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. No writing assistance was utilized in the production of this manuscript., (© 2020 Balaji Veeraraghavan.)

Background: Multidrug-resistant (MDR) E. coli with extended-spectrum β-lactamases (ESBLs) is becoming endemic in health care settings around the world. Baseline data on virulence and antimicrobial resistance (AMR) of specific lineages of E. coli circulating in developing countries like India is currently lacking., Methods: Whole-genome sequencing was performed for 60 MDR E. coli isolates. The analysis was performed at single nucleotide polymorphism (SNP) level resolution to identify the presence of their virulence and AMR genes., Results: Genome comparison revealed the presence of ST-131 global MDR and ST410 as emerging-MDR clades of E. coli in India. AMR gene profile for cephalosporin and carbapenem resistance differed between the clades. Genotypes blaCTX-M-15 and blaNDM-5 were common among cephalosporinases and carbapenemases, respectively. For aminoglycoside resistance, rmtB was positive for 31.7% of the isolates, of which 95% were co-harboring carbapenemases. In addition, the FimH types and virulence gene profile positively correlated with the SNP based phylogeny, and also revealed the evolution of MDR clones among the study population with temporal accumulation of SNPs. The predominant clone was ST167 (blaNDM lineage) followed by ST405 (global clone ST131 equivalent) and ST410 (fast spreading high risk clone)., Conclusions: This is the first report on the whole genome analysis of MDR E. coli lineages circulating in India. Data from this study will provide public health agencies with baseline information on AMR and virulent genes in pathogenic E. coli in the region., Competing Interests: The authors have declared that no competing interests exist.

The use of the harmonic regression model is well accepted in the epidemiological and biostatistical communities as a standard procedure to examine seasonal patterns in disease occurrence. While these models may provide good fit to periodic patterns with relatively symmetric rises and falls, for some diseases the incidence fluctuates in a more complex manner. We propose a two-step harmonic regression approach to improve the model fit for data exhibiting sharp seasonal peaks. To capture such specific behavior, we first build a basic model and estimate the seasonal peak. At the second step, we apply an extended model using sine and cosine transform functions. These newly proposed functions mimic a quadratic term in the harmonic regression models and thus allow us to better fit the seasonal spikes. We illustrate the proposed method using actual and simulated data and recommend the new approach to assess seasonality in a broad spectrum of diseases manifesting sharp seasonal peaks.

Recent findings demonstrate the origin of the plasmid-mediated colistin resistance gene mcr-3 from aeromonads. The present study aimed to screen for plasmid-mediated colistin resistance among 30 clinical multidrug-resistant (MDR) Aeromonas spp. PCR was used to screen for the presence of mcr-1 , mcr-2 , mcr-3 and mcr-4 , which revealed mcr-3 in a colistin-susceptible isolate (FC951). All other isolates were negative for mcr . Sequencing of FC951 revealed that the mcr-3 ( mcr-3.30 ) identified was different from previously reported variants and had 95.62 and 95.28 % nucleotide similarity with mcr-3.3 and mcr-3.10 . Hybrid assembly using IonTorrent and MinION reads revealed structural genetic information for mcr-3.30 with an insertion of IS As18 within the gene. Due to this, mcr-3.30 was non-expressive, which makes FC951 susceptible to colistin. Further, in silico sequence and protein structural analysis confirmed the new variant. To the best of our knowledge, this is the first report on a novel mcr-3 variant from India. The significant role of mcr -like genes in different Aeromonas species remains unknown and requires additional investigation to obtains insights into the mechanism of colistin resistance., Competing Interests: The authors declare that there are no conflicts of interest., (© 2020 The Authors.)

Aim: Shigella species has varying levels of virulence gene expression with respect to different sites of infection. In this study, the differential gene expression of S. dysenteriae in response to its site of infection was analyzed by transcriptomics., Methods: This study includes four clinical Shigella isolates. Transcriptomics was done for the stool and blood samples of a single patient. Isolates were screened for the presence of antimicrobial resistance genes., Results: The majority of genes involved in invasion were highly expressed in the strain isolated from the primary site of infection. Additionally, antimicrobial resistance ( dhfr 1A, sul II, bla OXA . bla CTX-M-1 and qnr S) genes were identified., Conclusion: This study provides a concise view of the transcriptional expression of clinical strains and provides a basis for future functional studies on Shigella spp., Competing Interests: Financial & competing interests disclosure The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. No writing assistance was utilized in the production of this manuscript., (© 2020 Balaji Veeraraghavan.)

The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance., (Copyright © 2020 American Society for Microbiology.)

Background: Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide., Methods: We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool., Results: K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae., Conclusions: K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.

Oxford Nanopore MinION sequencing technology has been gaining immense importance in identification of pathogen and antimicrobial resistance, though with 10-15% error rate. Short read technologies generates high accurate genome but with multiple fragments of genome. This study proposes a novel workflow to reduce the indels resulted from MinION long read sequencing by overlaying short read sequences from IonTorrent in the clinical isolates. Best of both techniques were employed which generated highly accurate-single chromosomal microbial genomes with increase in completeness of genomes from 44.5%, 30% and 43% to 98.6%, 98.6% and 96.6% for P. aeruginosa, A. veronii and B. pertussis respectively. To the best of our knowledge, this is the first study to generate a hybrid of IonTorrent and MinION reads to obtain single chromosomal genomes. This would enable to precisely infer both structural arrangement of genes and SNP based analysis for phylogenetic information., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Methicillin-resistant Staphylococcus aureus (MRSA) infection is an important clinical concern in patients, and is often associated with significant disease burden and metastatic infections. There is an increasing evidence of heterogeneous vancomycin-intermediate S. aureus (hVISA) associated treatment failure. In this study, we aim to understand the molecular mechanism of teicoplanin resistant MRSA (TR-MRSA) and hVISA. A total of 482 MRSA isolates were investigated for these phenotypes. Of the tested isolates, 1% were identified as TR-MRSA, and 12% identified as hVISA. A highly diverse amino acid substitution was observed in tcaRAB, vraSR, and graSR genes in TR-MRSA and hVISA strains. Interestingly, 65% of hVISA strains had a D148Q mutation in the graR gene. However, none of the markers were reliable in differentiating hVISA from TR-MRSA. Significant pbp2 upregulation was noted in three TR-MRSA strains, which had teicoplanin MICs of 16 or 32 μg/ml, whilst significant pbp4 downregulation was not noted in these strains. In our study, multiple mutations were identified in the candidate genes, suggesting a complex evolutionary pathway involved in the development of TR-MRSA and hVISA strains., Competing Interests: The authors have declared that no competing interests exist.

Objective: Resistance to colistin, a last resort antibiotic, has emerged in India. We investigated colistin-resistant Klebsiella pneumoniae(ColR-KP) in a hospital in India to describe infections, characterize resistance of isolates, compare concordance of detection methods, and identify transmission events., Design: Retrospective observational study., Methods: Case-patients were defined as individuals from whom ColR-KP was isolated from a clinical specimen between January 2016 and October 2017. Isolates resistant to colistin by Vitek 2 were confirmed by broth microdilution (BMD). Isolates underwent colistin susceptibility testing by disk diffusion and whole-genome sequencing. Medical records were reviewed., Results: Of 846 K. pneumoniae isolates, 34 (4%) were colistin resistant. In total, 22 case-patients were identified. Most (90%) were male; their median age was 33 years. Half were transferred from another hospital; 45% died. Case-patients were admitted for a median of 14 days before detection of ColR-KP. Also, 7 case-patients (32%) received colistin before detection of ColR-KP. All isolates were resistant to carbapenems and susceptible to tigecycline. Isolates resistant to colistin by Vitek 2 were also resistant by BMD; 2 ColR-KP isolates were resistant by disk diffusion. Moreover, 8 multilocus sequence types were identified. Isolates were negative for mobile colistin resistance (mcr) genes. Based on sequencing analysis, in-hospital transmission may have occurred with 8 case-patients (38%)., Conclusions: Multiple infections caused by highly resistant, mcr-negative ColR-KP with substantial mortality were identified. Disk diffusion correlated poorly with Vitek 2 and BMD for detection of ColR-KP. Sequencing indicated multiple importation and in-hospital transmission events. Enhanced detection for ColR-KP may be warranted in India.

Systematically collected hospitalization records provide valuable insight into disease patterns and support comprehensive national infectious disease surveillance networks. Hospitalization records detailing patient's place of residence (PoR) can be utilized to better understand a hospital's case load and strengthen surveillance among mobile populations. This study examined geographic patterns of patients treated for cholera at a major hospital in south India. We abstracted 1401 laboratory-confirmed cases of cholera between 2000-2014 from logbooks and electronic health records (EHRs) maintained by the Christian Medical College (CMC) in Vellore, Tamil Nadu, India. We constructed spatial trend models and identified two distinct clusters of patient residence-one around Vellore (836 records (61.2%)) and one in Bengal (294 records (21.5%)). We further characterized differences in peak timing and disease trend among these clusters to identify differences in cholera exposure among local and visiting populations. We found that the two clusters differ by their patient profiles, with patients in the Bengal cluster being most likely older males traveling to Vellore. Both clusters show well-aligned seasonal peaks in mid-July, only one week apart, with similar downward trend and proportion of predominant O1 serotype. Large hospitals can thus harness EHRs for surveillance by utilizing patients' PoRs to study disease patterns among resident and visitor populations.

Melioidosis caused by Burkholderia pseudomallei has become an important clinical threat, especially in Northern Australia and Southeast Asia. However, the genome information on this pathogen is limited. B. pseudomallei isolates identified from bloodstream infections from inpatients were subjected to whole-genome sequencing by IonTorrent PGM and MinION Oxford Nanopore sequencing technologies. Highly accurate complete genomes of two strains, VB3253 and VB2514, were obtained by a hybrid genome assembly method using both short and long DNA reads. Both isolates carried bla PenI and carbapenemase-encoding bla OXA-57 genes, although the isolates were susceptible to imipenem by E-test method with MIC 1 μg/mL. Multiple IS family transposases specific for all non-fermenting Gram-negative bacteria (NFGNBs)-especially IS3 and IS5, which facilitate mobilization of extended-spectrum β-lactamase (ESBL) and carbapenemase genes-were carried in these genomes. This further adds to the complexity of gene transmission. These IS families were identified only upon hybrid genome assembly and would otherwise be missed., (© 2019 Published by Elsevier Ltd.)

Purpose: To investigate the epidemiology of invasive pneumococcal disease (IPD), prevalent serotypes, and pattern of antimicrobial resistance (AMR) in Indian adults., Methods: Prospective laboratory based surveillance of IPD was carried out in >18 years age group between January 2007 and July 2017, from a tertiary care hospital in South India. All Streptococcus pneumoniae culture positives from blood, CSF and sterile body fluids were characterized to identify the serotypes and AMR., Results: A total of 408 IPD cases were characterized in this study. The overall case fatality rate in this study was 17.8% (95% confidence interval (CI): 14.1, 22.4). Pneumonia (39%), meningitis (24.3%), and septicaemia (18.4%) were the most common clinical conditions associated with IPD. Serotypes 1, 3, 5, 19F, 8, 14, 23F, 4, 19A and 6B were the predominant serotypes in this study. Penicillin non-susceptibility was low with 6.4% CONCLUSION: Serotype data from this study helped in accurate estimation of pneumococcal conjugate vaccine-13 and pneumococcal polysaccharide vaccine-23 protective coverage against serotypes causing IPD in India as 58.7% (95% CI: 53.8, 63.4) and 67.4% (95% CI: 62.7, 71.8) respectively. Penicillin non-susceptibility in meningeal IPD cases is 27.4%. Empirical therapy for meningeal IPD must be cephalosporin in combination with vancomycin since cefotaxime non-susceptibility in meningeal IPD is 9.9., (Copyright © 2018. Published by Elsevier B.V.)

Staphylococcus aureus is of significant clinical concern in both community- and hospital-onset infections. The key to the success of S. aureus as a pathogen is its ability to swiftly develop antimicrobial resistance. Methicillin-resistant S. aureus (MRSA) is not only resistant to nearly all beta-lactams but also demonstrates resistance to several classes of antibiotics. A high prevalence of MRSA is seen across worldwide. For many decades, vancomycin remained as gold standard antibiotic for the treatment of MRSA infections. In the past decades, linezolid, daptomycin, ceftaroline and telavancin received regulatory approval for the treatment of infections caused by resistant Gram-positive pathogens. Although these drugs may offer some advantages over vancomycin, they also have significant limitations. These includes vancomycin's slow bactericidal activity, poor lung penetration and nephrotxicity;linezolid therapy induced myelosuppression and high cost of daptomycin greatly limits their clinical use. Moreover, daptomycin also gets inactivated by lung naturally occurring surfactants. Thus, currently available therapeutic options are unable to provide safe and efficacious treatment for those patients suffering from hospital-acquired pneumonia, bloodstream infections (BSIs), bone and joint infections and diabetic foot infections (DFI). An unmet need also exists for a safe and efficacious oral option for switch-over convenience and community treatment. Herein, the review is intended to describe the supporting role of anti-staphylococcal antibiotics used in the management of S. aureus infections with a special reference to levonadifloxacin. Levonadifloxacin and its prodrug alalevonadifloxacin are novel benzoquinolizine subclass of quinolone with broad-spectrum of anti-MRSA activity. It has been recently approved for the treatment of complicated skin and soft-tissue infection as well as concurrent bacteraemia and DFI in India., Competing Interests: None

Salmonella Typhimurium ST313 is known to cause invasive disease in sub Saharan African (sSA) countries while the same sequence type is often associated with gastro-intestinal infections in the UK and Brazil. Although S. Typhimurium has been frequently isolated from human samples in India, the prevalence and invasive nature of infection of ST313 is currently unknown. The present study elucidates the phenotypic and genotypic characteristics of S. Typhimurium strain B3589 that belongs to ST313. The isolate was subjected to serotyping and antimicrobial susceptibility test to understand its phenotypical characteristics. Whole genome sequencing and comparative genomic analysis was carried out to provide an insight into S. Typhimurium ST313 lineage in India. The results suggests antibiotic resistance against aminoglycoside was associated with the presence of aminoglycoside modifying enzymes aac(6')-Ia in the genome. Phylogenetic analysis revealed the India-ST313 isolates are genotypically distinct from the known African, UK and Brazilian ST313 lineages. The isolate possess the characteristic prophage gene repertoire except BTP-5. The presence of BTP-1 and more importantly bstA virulence gene has been the distinguishable feature of strain B3589 among other non-African isolates. In addition the genome degradation of African ST313 lineage-2 was not conserved in the Indian ST313 isolates. Fewer genome degradation events as well as the absence of plasmid mediated MDR locus suggest the Indian ST313 isolates are of low risk. The identification of ST313 isolates in India reveals the previously unknown characteristics of ST313 S. Typhimurium isolated from India., (Copyright © 2019 Elsevier B.V. All rights reserved.)

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., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objectives: Recently, the virulence factor sasX was described on the mobile genetic element φSPβ prophage in a ST239-SCCmecIII methicillin-resistant Staphylococcus aureus (MRSA) clone. The aim of this study was to identify sesI, an sasX homologue, in an MRSA ST239 strain., Methods: MRSA strain VB1490 was isolated from a patient with MRSA bacteraemia in India. Staphylococcal cassette chromosomemec (SCCmec) typing and whole-genome shotgun sequencing were performed. Phylogenetic analysis of VB1490 and ST239 reference genomes from the NCBI database was performed. Amplification and sequencing of the sasX gene was performed to establish allele homology., Results: The sasX gene identified in isolate VB1490 was more similar to the sesI gene of Staphylococcus epidermidis RP62A than the sasX gene of ST239 MRSA strain. Whole-genome analysis revealed the presence of the sasX gene on a φSPβ-like prophage that exhibited high sequence identity to that of S. epidermidis strain RP62A., Conclusion: These finding suggests the dissemination of the invasion-determining virulence factorsesI from S. epidermidis to a ST239 MRSA strain., (Copyright © 2019. Published by Elsevier Ltd.)

Background : The increasing burden of carbapenem-resistant Enterobacteriaceae (CRE) carriage and infection in different patient settings in India has created an acute need for guidance for clinicians regarding optimal strategies for the management of CRE infection in critically ill patients. Research design and methods : A multidisciplinary panel of 11 Indian experts in CRE infection assembled for comprehensive discussion and consensus development. The experts developed clinical statements through a systematic review of key literature. Main outcome measures : The panel voted anonymously on 60 clinically relevant questions, through a modified Delphi process. Results : Forty-six key clinical consensus statements (CCS) were proposed. The panel reached a consensus on several important issues, providing recommendations on surveillance, diagnosis, prevention, pharmacokinetic challenges, combination therapy, and cornerstone molecules in CRE infections. The panel also proposed a treatment algorithm for NDM-prevalent settings. Conclusion : These consensus statements may offer clinicians expert guidance on the management of CRE infections. There is a dearth of high-/moderate-level evidence on managing CRE infections; the recommendations presented herein are based on expert opinion.

Background: Streptococcus pneumoniae is a major cause of pneumonia, meningitis, and other serious infections among children in India. India introduced the 13-valent pneumococcal conjugate vaccine (PCV) in several states in 2017, and is expected to expand to nationwide coverage in the near future. To establish a baseline for measuring the impact of PCV in India, we assessed overall and serotype-specific nasopharyngeal carriage in two pediatric populations., Methods: A cross-sectional study was conducted in Palwal District, Haryana, from December 2016 to July 2017, prior to vaccine introduction. Children 2-59 months of age with clinical pneumonia seeking healthcare and those in the community with no clear illness were targeted for enrollment. A nasopharyngeal swab was collected and tested for pneumococcus using conventional culture and sequential multiplex PCR. Isolates were tested for antimicrobial resistance using an E test. Children were considered colonized if pneumococcus was isolated by culture or PCR. The prevalence of pneumococcal and serotype-specific colonization was compared between groups of children using log-binomial regression., Results: Among 601 children enrolled, 91 had clinical pneumonia and 510 were community children. The proportion colonized with S. pneumoniae was 74.7 and 54.5% among children with clinical pneumonia and community children, respectively (adjusted prevalence ratio: 1.38; 95% confidence interval: 1.19, 1.60). The prevalence of PCV13 vaccine-type colonization was similar between children with clinical pneumonia (31.9%) and community children (28.0%; p = 0.46). The most common colonizing serotypes were 6A, 6B, 14, 19A, 19F, and 23F, all of which are included in the PCV13 vaccine product. Antimicrobial resistance to at least one drug was similar between isolates from children with clinical pneumonia (66.1%) and community children (61.5%; p = 0.49); while resistance to at least two drugs was more common among isolates from children with clinical pneumonia (25.8% vs. 16.4%; p = 0.08). Resistance for all drugs was consistently higher for PCV13 vaccine-type serotypes compared to non-vaccine serotypes in both groups., Conclusion: This study provides baseline information on the prevalence of serotype-specific pneumococcal colonization among children prior to the introduction of PCV in India. Our results suggest a role for pneumococcal vaccines in reducing pneumococcal colonization and antimicrobial resistant isolates circulating in India.

Background: Pneumococcal pneumonia is one of the major causes of mortality in children less than 5 years in Asia, especially in India. Available PCVs have less serotype coverage in India compared to western countries. Moreover, the baseline pneumococcal serotype and sequence type data is limited and available data doesn't represent the entire India. With this background we aimed to characterize invasive and carriage isolates of S. pneumoniae from a tertiary care hospital in South India., Materials and Methods: A total of 221 S. pneumoniae isolates, invasive (n=138) and carriage (n=83) between the time period of 2012-2018 were included. Isolates was identified and confirmed using standard laboratory protocols. Serotyping was performed by Customized sequential multiplex PCR and MLST as described in www.pubmlst.org., Results: The major serotypes were 19F, 6B, 14, 6A and 19A and the sequence types (ST) were ST63, 236 and 230. Predominant STs in invasive was ST 63 whereas in carriage were ST4894 and 1701. High level ST diversity in carriage was observed. Majority of the STs were SLVs or DLVs of previously reported STs or PMEN clones. Phylogenetic analyses of the STs revealed gradual expansion of three PMEN CCs CC320, 63 and 230., Conclusion: The vaccine serotypes were the predominant ones found to be associated with IPD, PMEN clones, new STs and antimicrobial resistance. Accordingly, PCV13 is expected to provide invasive serotype coverage of 75% in Indian children less than 5 years. This study provides baseline serotype and sequence type data prior to the introduction of PCV in South India., Competing Interests: None

Diphtheria is a dreadful disease caused by Corynebacterium diphtheriae. Lysogenised bacteriophages carrying toxin gene in C. diphtheriae can make the strain toxigenic. However, such phage disseminates the toxin genes to other strains when it undergoes lytic phase. As little is known about the phage diversity in C. diphtheriae in India, the present study was undertaken to investigate the prophages integrated into the genome of 29 clinical isolates of C. diphtheriae using whole-genome shotgun sequencing. Amongst these isolates, 27 were toxigenic, while 2 were non-toxigenic strains. Of the 27 toxigenic strains, all harbored known phages carrying toxin gene and two other phages with unknown function. However, the two non-toxin strains did not harbour any of the phages in the genome. It is imperative to devise prevention strategies that hinder the dissemination of toxin by prophages, as it may increase the complications of diphtheria post-immunisation., Competing Interests: None

Introduction: Antimicrobial-resistant HAI (Healthcare associated infection) are a global challenge due to their impact on patient outcome. Implementation of antimicrobial stewardship programmes (AMSP) is needed at institutional and national levels. Assessment of core capacities for AMSP is an important starting point to initiate nationwide AMSP. We conducted an assessment of the core capacities for AMSP in a network of Indian hospitals, which are part of the Global Health Security Agenda-funded work on capacity building for AMR-HAIs., Subjects and Methods: The Centers for Disease Control and Prevention's core assessment checklist was modified as per inputs received from the Indian network. The assessment tool was filled by twenty hospitals as a self-administered questionnaire. The results were entered into a database. The cumulative score for each question was generated as average percentage. The scores generated by the database were then used for analysis., Results and Conclusion: The hospitals included a mix of public and private sector hospitals. The network average of positive responses for leadership support was 45%, for accountability; the score was 53% and for key support for AMSP, 58%. Policies to support optimal antibiotic use were present in 59% of respondents, policies for procurement were present in 79% and broad interventions to improve antibiotic use were scored as 33%. A score of 52% was generated for prescription-specific interventions to improve antibiotic use. Written policies for antibiotic use for hospitalised patients and outpatients were present on an average in 72% and 48% conditions, respectively. Presence of process measures and outcome measures was scored at 40% and 49%, respectively, and feedback and education got a score of 53% and 40%, respectively. Thus, Indian hospitals can start with low-hanging fruits such as developing prescription policies, restricting the usage of high antibiotics, enforcing education and ultimately providing the much-needed leadership support., Competing Interests: None

Acinetobacter species have emerged as one of the most clinically important pathogens. The phenotypic techniques which are currently available are insufficient in accurately identifying and differentiating the closely related and clinically important Acinetobacter species. Here, we discuss the advantages and limitations of the conventional phenotypic methods, automated identification systems, molecular methods and MALDI-TOF in the precise identification and differentiation of Acinetobacter species. More specifically, several species of this genus are increasingly reported to be of high clinical importance. Molecular characterization such as of bla OXA-51 -like PCR together with rpoB sequencing has high discriminatory power over the conventional methods for Acinetobacter species identification, especially within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex., Competing Interests: Financial & competing interests disclosure The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. No writing assistance was utilized in the production of this manuscript.

Background: Recently, in India, there has been a shift from NDM to OXA48-like carbapenemases. OXA-181 and OXA-232 are the frequently produced variants of OXA48-like carbapenemases. OXA48-like carbapenemases are also known to be carried on transposons such as Tn1999, Tn1999.2 and it is also associated with IS1R carried on Tn1999. In India, there are no previous reports studying the association of mobile genetic elements (MGEs) with OXA48-like carbapenemases. The present study was aimed at determining the genetic backbone of OXA48-like carbapenemases to determine the role of MGEs in its transfer and to investigate the Inc plasmid type carrying bla OXA48-like ., Results: A total of 49 carbapenem resistant K. pneumoniae which included 25 isolates from South India and 24 isolates from North India, were included in the study. Whole genome sequencing using Ion Torrent PGM was performed to study the isolates. OXA-232 was present in 35 isolates (71%). In 19 isolates (39%), bla OXA48-like was associated with MGEs. Insertion sequences such as ISX4, IS1, IS3, ISKpn1, ISKpn26, ISKpn25, ISSpu2, ISKox1, IS4321R, ISEc36, and ISPa38; and transposons such as TnAs3 and Tn2, were present. Isolates from northern and southern India belonging to same sequence type (ST) had diverse genetic backbone for bla OXA48-like . ST14 isolates from north had IS5 and Tn3 families while from south they had IS1, IS5 and IS630 families. ST231 from north had IS5, IS6 and Tn3 families with bla OXA-232 while from south, IS1, IS3 and IS5 families were observed; with ISKpn26 being present among isolates from both the regions. bla OXA48-like was predominantly found on ColKP3 plasmid. ST231 was the predominant ST in 22 isolates (45%)., Conclusion: OXA-232 is the predominant variant of OXA48-like carbapenemase with ST231 being the commonest ST of OXA48-like carbapenemase producing K. pneumoniae in India. Diverse MGEs have been associated with both bla OXA-232 and bla OXA-181 which contribute to their spread. The MGEs in the present study are different from those reported earlier. There is no clonal expansion of bla OXA48-like producing K. pneumoniae since diverse STs were observed. Monitoring the genetic backbone of OXA48-like carbapenemase is essential to better understand the transmission dynamics of XDR K. pneumoniae.

Introduction: The last few years have seen the emergence of multi-drug resistant (MDR) Gram-negative infections, which are associated with high morbidity and mortality. The indiscriminate use of colistin has led to the development of resistance, which can be diagnosed effectively by broth microdilution. Studies from India are limited, and this study was conducted in order to determine the prevalence and risk factors associated with colistin resistance., Methods: Urine samples from patients admitted with urinary tract infection (UTI), growing MDR Escherichia coli and Klebsiella pneumoniae, were tested for the minimum inhibitory concentration (MIC) of colistin by broth microdilution. Isolates with an MIC >2 µg ml -1 (resistant) were subjected to polymerase chain reaction (PCR) for the mcr1, mcr2 and mgrB genes. A case-control study with 21 cases (resistant) and 42 matched controls (sensitive) was designed to evaluate risk factors and outcomes (recurrent UTI, readmission and hospital stay >2 weeks)., Results: Two hundred and fifty MDR isolates (E. coli=142/2319 and K.pneumoniae=108/775) from 216 patients were selected from the 25 046 isolates screened. Twenty-five isolates (20 K.pneumoniae and 5 E. coli) were resistant to colistin, with a prevalence of 3.52  % in E. coli and 18.5  % in K. pneumoniae among the MDR isolates. PCR for the mcr1 and mcr2 genes was negative. Multivariate regression showed that multiple episodes of hospitalization, hospital stay >2 weeks, exposure to >three antibiotic classes and abnormality/surgery of the lower urinary tract were the significant risk factors for colistin resistance. Previous use of colistin and colistin resistance had a significant effect on all outcomes., Conclusions: K. pneumoniae show six times higher prevalence of colistin resistance than E. coli, and the emergence of resistant organisms has led to an increase in morbidity in infected patients.

Multi-drug resistance and transfer of mobile genetic elements among enteric pathogens is being reported to have increased rapidly. Commensal Escherichia coli was previously known to acquire mobile genetic elements from other genus/species. E. coli is also capable of disseminating these elements containing antimicrobial resistance determinants through horizontal transfer. Similarly, for Shigellae the antimicrobial resistance are on rise for fluoroquinolones and cephalosporins due to accumulation of mobile elements. Thus the study was hypothesized to investigate the role of transferable plasmids in commensal MDR E. coli vs Salmonella spp, and MDR Shigella flexneri vs Salmonella spp. pKP3-A plasmid containing qnrS1 was successfully transferred from E. coli to Salmonella spp. Similarly, a plasmid containing qnrS1 and bla CTX-M-15 was transferred from Shigella to Salmonella spp. However, bla CTX-M-15 was not transferred from E. coli as it was integrated into chromosome that was revealed by next-generation sequencing. This might be a reason that fluoroquinolone-resistant determinants are more frequently transferred than the cephalosporin resistant determinants. Findings from the study emphasize that mobile elements with AMR determinants are significant public health concern that has potential to rapidly disseminate.

Shigella is the major cause of bacillary dysentery worldwide, especially in developing countries. There are several virulence factors essential for the organism to be virulent which are generally present in the virulence plasmid and on chromosomal pathogenicity islands. The present study was undertaken to determine the virulence gene profile of Shigella spp isolated from a clinical specimen and to study their significant association with common clinical symptoms and antimicrobial resistance. Sixty Shigella whole genome sequences, including 22 S. flexneri , 14 S. sonnei , 17 S. boydii and 7 S. dysenteriae were analyzed for the presence of virulence genes. The gene found predominantly in this study were ipa H (90%) followed by sig A (83%), and lpf A (78%) respectively. The virulence genes were significantly higher in S. flexneri , particularly in serotype 2 compared to S. sonnei . Interestingly, a significant association was observed between sig A gene and fever whereas sep A and sig A were found to be associated with diarrhea. Among the studied Shigella isolates, the presence of virulence genes was found higher in isolates resistant to more than three antibiotic classes. The present work revealed the varying incidence of virulence determinants among different Shigella serogroups and shows their contribution to disease severity.

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 bla KPC-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 bla OKP-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.

Objective: Antimicrobial stewardship programs (ASPs) are effective in developed countries. In this study, we assessed the effectiveness of an infectious disease (ID) physician-driven post-prescription review and feedback as an ASP strategy in India, a low middle-income country (LMIC)., Design and Setting: This prospective cohort study was carried out for 18 months in 2 intensive care units of a tertiary-care hospital, consisting of 3 phases: baseline, intervention, and follow up. Each phase spanned 6 months., Participants: Patients aged ≥15 years receiving 48 hours of study antibiotics were recruited for the study., Methods: During the intervention phase, an ID physician reviewed the included cases and gave alternate recommendations if the antibiotic use was inappropriate. Acceptance of the recommendations was measured after 48 hours. The primary outcome of the study was days of therapy (DOT) per 1,000 study patient days (PD)., Results: Overall, 401 patients were recruited in the baseline phase, 381 patients were recruited in the intervention phase, and 379 patients were recruited in the follow-up phase. Antimicrobial use decreased from 831.5 during the baseline phase to 717 DOT per 1,000 PD in the intervention phase (P &lt; .0001). The effect was sustained in the follow-up phase (713.6 DOT per 1,000 PD). De-escalation according to culture susceptibility improved significantly in the intervention phase versus the baseline phase (42.7% vs 23.6%; P &lt; .0001). Overall, 73.3% of antibiotic prescriptions were inappropriate. Recommendations by the ID team were accepted in 60.7% of the cases., Conclusion: The ID physician-driven implementation of an ASP was successful in reducing antibiotic utilization in an acute-care setting in India.

The emerging antimicrobial resistance leading to gram-positive infections (GPIs) is one of the major public health threats worldwide. GPIs caused by multidrug resistant bacteria can result in increased morbidity and mortality rates along with escalated treatment cost and hospitalisation stay. In India, GPIs, particularly methicillin-resistant Staphylococcus aureus (MRSA) prevalence among invasive S. aureus isolates, have been reported to increase exponentially from 29% in 2009 to 47% in 2014. Apart from MRSA, rising prevalence of vancomycin-resistant enterococci (VRE), which ranges from 1 to 9% in India, has raised concerns. Moreover, the overall mortality rate among patients with multidrug resistant GPIs in India is reported to be 10.8% and in ICU settings, the mortality rate is as high as 16%. Another challenge is the spectrum of adverse effects related to the safety and tolerability profile of the currently available drugs used against GPIs which further makes the management and treatment of these multidrug resistant organisms a complex task. Judicious prescription of antimicrobial agents, implementation of antibiotic stewardship programmes, and antibiotic policies in hospitals are essential to reduce the problem of drug-resistant infections in India. The most important step is development of newer antimicrobial agents with novel mechanisms of action and favourable pharmacokinetic profile. This review provides a synopsis about the current burden, treatment options, and the challenges faced by the clinicians in the management of GPIs such as MRSA , Quinolone-resistant Staphylococcus, VRE, and drug-resistant pneumococcus in India.

Purpose: Hospital outbreaks are observed increasingly worldwide with various organisms from different sources such as contaminated ultrasound gel, intravenous (IV) fluids and IV medications. Among these, ultrasound gel is one of the most commonly reported sources for Burkholderia cepacia complex (Bcc) outbreaks. In this study, we describe our experience on investigation and the management of Bcc bacteraemia outbreak due to contaminated ultrasound gel from a tertiary care centre, South India., Materials and Methods: Over a 10-day period in October 2016, seven children in our Paediatric intensive care unit (ICU) were found to have bacteraemia with Bcc isolated from their blood culture. Repeated isolation of the same organism with similar antimicrobial susceptibility pattern over a short incubation period from the same location, confirmed the outbreak. An active outbreak investigation, including environmental surveillance, was carried out to find the source and control the outbreak. Isolates were subjected to multi-locus sequence typing (MLST) and global eBURST (goeBURST) analysis., Results: Environmental surveillance revealed contaminated ultrasound gel as the source of infection. MLST and goeBURST analysis confirmed that the outbreak was caused by a novel sequence type 1362 with the same clonal complex CC517. The outbreak was controlled by stringent infection control measures, withdrawal of contaminated ultrasound gel from regular usage and implementing the practice of using ultrasonogram (USG) probe cover for USG screening and guided procedures., Conclusion: This report highlights the importance of early identification of an outbreak, prompt response of the ICU and infection control teams, sound environmental and epidemiological surveillance methods to identify the source and stringent infection control measures to control the outbreak. Contaminated ultrasound gel can be a potential source for healthcare-associated infection, which cannot be overlooked., Competing Interests: None

India is one among the four Asian countries with the greatest number of deaths due to pneumococcal infection among children under 5 years. pneumococcal conjugate vaccine (PCV) has been introduced in a phased manner in five major Indian states. Ambiguity remains in choosing the appropriate type of PCV and optimum schedule with maximum effectiveness specific for each country. Here, we discuss the evidences with respect to serotype coverage, immunogenicity, reactogenicity and dosage schedule for introduction of PCV13 in India. In addition, the expected PCV impact and the challenges are detailed. PCV13 is expected to provide >75% serotype coverage for invasive pneumococcal disease (IPD) serotypes in Indian children combined with the replacement by nonvaccine serotypes which is unpredictable due to lack of complete data. Nasopharyngeal (NP) surveillance is easy, feasible and can replace IPD surveillance in resource-poor settings. Continuous IPD as well as NP surveillance in all the regions are necessary to assess the impact of PCV in India., Competing Interests: None

Staphylococcal surface protein sasX is a colonization mediating virulence factor in ST239 methicillin-resistant Staphylococcus aureus (MRSA) strains, which potentially contribute to its successful establishment. We aimed to study the presence and dissemination of sasX in clinical MRSA isolates and among MRSA carriers. A total of 450 nonduplicate clinical MRSA isolates recovered from blood cultures between 2013 and 2017 were included in this study. In addition, 93 nasal swabs were collected from patients receiving hemodialysis, after obtaining consent and screening for MRSA colonization. sasX polymerase chain reaction and sequencing were carried out for all isolates. Multilocus sequence typing was performed for all sasX-positive isolates. Of the tested clinical MRSA isolates, 11% (n = 48) were positive for sasX gene. Among hemodialysis patients, 26% (n = 24) were characterized as MRSA carriers. However, all MRSA strains isolated from nasal swab were negative for sasX gene. Overall, we observed 10% (11% in clinical MRSA isolates and 0% in MRSA carriers) of sasX-positive MRSA in this study. ST239 and ST368 were the predominant sasX carrying MRSA lineages. The majority of sasX carrying MRSA strains were characterized as Staphylococcus epidermidis surface protein I (sesI; 71%), a sasX homolog native to S. epidermidis. This study highlights the dissemination of sasX/sesI to ST368 (CC8), ST3324 (CC8), ST772 (CC1), and ST22 (CC22). The presence of S. epidermidis-specific invasive factor sesI in clinical MRSA strains provides evidence for horizontal transfer between these closely related species.

Background: Non-typhoidal Salmonella (NTS) infection is a serious public health problem globally. Although NTS infections are self-limited, antimicrobial therapy is recommended for severe infections and immunocompromised patients. Antimicrobial resistance (AMR) in these pathogens further limits its therapeutic options. Here, we report an incidence of ceftriaxone resistance in NTS over the past 9 years in a southern Indian region., Materials and Methods: Molecular mechanisms of resistance in ceftriaxone-resistant NTS have been tested by both phenotypic and molecular methods. Minimum inhibitory concentration was determined by the E-test and broth microdilution method. AMR gene markers of β-lactamases such as AmpCs (bla MOX , bla CMY , bla DHA , bla FOX , bla ACC and bla ACT ) and extended-spectrum β-lactamases (ESBLs) (bla SHV , bla TEM , bla VEB , bla PER , bla CTXM-1 like, bla CTXM-2 like , bla CTXM-8 like , bla CTXM-9 like and bla CTXM-25 like ) were screened. The presence of IncH12 and IncI1 plasmid was also analysed., Results: The study reports a 5% prevalence of ceftriaxone resistance in NTS. The most common serogroup was Salmonella Group B followed by Salmonella Group E and Salmonella group C1/C2. The occurrence of bla CTX-M-1 , bla TEM , bla CMY and bla SHV genes was observed in 54%, 54%, 48% and 3% of the isolates, respectively. Interestingly, few isolates carried dual resistance genes (ESBLs and AmpCs). IncH12 and IncI1 plasmid was identified in isolates carrying ESBL and AmpC genes, respectively., Conclusion: This study shows that ceftriaxone resistance is mainly mediated by β-lactamases such as ESBL and AmpC. As the incidence of ceftriaxone resistance is rising gradually over the years, it is imperative to monitor the AMR in this species., Competing Interests: None

Introduction: Tigecycline Evaluation and Surveillance Trail (TEST) study is an on-going global surveillance. The study was performed to determine the susceptibility of common pathogens to tigecycline and comparator antibiotics by broth microdilution (BMD) at two tertiary care centres in India from 2015 to 2017., Methodology: Total of 989 isolates collected from various clinical specimens between January 2015 and September 2017 from two centres in India were included. BMD was performed to determine the minimum inhibitory concentration (MIC) for tigecycline and comparator antibiotics., Results: Among Gram-negative bacteria, susceptibility to tigecycline was lowest among Klebsiella spp. being 84% while others such as E. coli, Enterobacter spp., Serratia spp. and H. influenzae showed susceptibility of 98%, 95%, 98% and 100% respectively. Overall, 99 isolates among Enterobacteriaceae (E. coli, Klebsiella spp. and Enterobacter spp.) were ESBL producers, susceptible to tigecycline. Among the 101 meropenem resistant Enterobacteriaceae, 85 were susceptible to tigecycline (84%). Among the Gram-positive bacteria, S. aureus and Enterococcus spp. were 99% and 98% susceptible to tigecycline respectively. Among 68 MRSA isolates in the study, 66 (97%) were susceptible to tigecycline. Seven vancomycin resistant E. faecalis were isolated and all were susceptible to tigecycline., Conclusion: Tigecycline has retained activity over both Gram-positive and Gram-negative organisms with MIC values comparable to global reports. About 98% of the MDR Gram-positive and Gram-negative bacteria in the study are susceptible to tigecycline. With increased incidence of extensively drug resistant organisms, tigecycline is a potential reserve drug., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2019 Balaji Veeraraghavan, Aruna Poojary, Chaitra Shankar, Anurag Kumar Bari, Seema Kukreja, Bhuvaneswari Thukkaram, Ramya Gajaraj Neethimohan, Yamuna Devi Bakhtavachalam, Shweta Kamat.)

Introduction: Heteroresistant vancomycin-intermediate Staphylococcus aureus (hVISA) bacteremia may result in clinical failure of vancomycin therapy, together with prolonged infection and hospitalization. This clinical problem has resulted in a search for more effective treatment options. The current study was designed to further investigate the synergistic effect of oxacillin plus vancomycin against methicillin-resistant S. aureus (MRSA) and hVISA using checkerboard and time-kill assays., Methods: Non-duplicate S. aureus isolates including hVISA (n = 29), MRSA (n = 10) and methicillin susceptible S. aureus (MSSA, n = 11) were used for combinational testing using checkerboard and time-kill assays., Results: Twenty-one isolates, 15 hVISA and 6 MRSA, showed synergy between oxacillin and vancomycin by checkerboard assay with fractional inhibitory concentration indices of ≤ 0.5. The addition of oxacillin to vancomycin resulted in a reduction in baseline vancomycin MIC from 1-2 to 0.06-0.5 µg/ml against MRSA and hVISA isolates. In the time-kill assay, the combination of oxacillin and vancomycin resulted in synergistic activity against hVISA (n = 23) and MRSA (n = 7) isolates. Regrowth was observed in six hVISA isolates exposed to combination in the time-kill assay, but none of them reached the original inoculum density at 24 h. All re-growth isolates showed a onefold increase in vancomycin MIC (from 1 to 2 µg/ml) and were re-confirmed as hVISA using the population-analysis profile experiment. Overall, for hVISA and MRSA, the combination of oxacillin plus vancomycin had greater antibacterial effect than each individual drug alone., Conclusion: The present study showed the potential activity of vancomycin plus oxacillin combination against hVISA and MRSA isolates. Further, continued evaluation of this combination is warranted and may have therapeutic benefits in treating complicated MRSA infections.

Objectives: Plasmids harbouring antimicrobial resistance determinants in clinical strains are a significant public-health concern worldwide. The present study investigated such plasmids in clinical isolates of Shigella flexneri., Methods: A total of 162 Shigella isolates were obtained from stool specimens in the year 2015. Among the 70 multidrug-resistant (MDR) Shigella spp., 27 S. flexneri isolates were randomly selected for further characterisation. Antimicrobial resistance genes (ARGs) and plasmid incompatibility (Inc) types were analysed., Results: IncFII plasmids were found in 63% (17/27) of the studied S. flexneri isolates. ARGs such as dhfr1a (81%), sulII (74%), bla OXA (74%), bla TEM (33%), bla AmpC (30%), qnrS (15%) and qnrB (4%) were identified by PCR, whereas bla CTX-M was not detected. Next-generation sequencing of a representative S. flexneri IncFII-type plasmid (pSF470) revealed the presence of bla TEM1-B , bla DHA-1 , qnrB10, mphA, sulI, sulII, strA, strB and tetR ARGs along with the intI1 integrase gene. In addition, pMLST analysis showed that the replicon belonged to F2:A-:B- type., Conclusions: This study helps to know the prevalent plasmid types in MDR Shigella isolates and will improve our understanding of resistance dissemination among enteric bacteria. ARGs in plasmids further highlight the importance of such studies in enteric bacteria., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Numerous previous publications on the detection of bacterial isolates harbouring the mcr-1 gene from animals and humans strongly suggest an underlying route of transmission of colistin resistance via the food chain. The aim of this study was to investigate the presence of colistin-resistant (Col-R) bacteria in Indian food samples and to identify the underlying mechanisms conferring colistin resistance., Methods: Raw food material, including poultry meat, mutton meat, fish, fruit and vegetables, collected from food outlets in Chennai, India, were processed to identify Col-R bacteria using eosin methylene blue agar supplemented with colistin. Colistin minimum inhibitory concentrations (MICs) were determined by the broth microdilution method. PCR for the mcr-1 and mcr-3 genes was performed on Col-R Escherichia coli and Klebsiella pneumoniae isolates. Mutations in the mgrB gene were analysed in K. pneumoniae isolates. One representative mcr-1-positive E. coli was subjected to whole-genome sequencing., Results: Of 110 food samples tested, 51 (46.4%) were positive for non-intrinsic Col-R Gram-negative bacteria. Three E. coli isolates were found to harbour mcr-1, whereas none were positive for mcr-3. Ten K. pneumoniae isolates had alterations in mgrB, with mutations in four and insertional inactivation in six., Conclusion: The presence of Col-R bacteria and the mcr-1 gene in raw food samples further complicates the antimicrobial resistance scenario in India. To the best of our knowledge, this is the first report in the global literature on mgrB mutation and its insertional inactivation conferring Col-R in K. pneumoniae from food samples., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objective: Melioidosis being an important cause of community-acquired sepsis, caused by Burkholderia pseudomallei in the tropical and subtropical countries, is often underreported or misinterpreted on imaging investigations. We aim to describe the spectrum of imaging manifestations of melioidosis and to evaluate its role in prognosticating clinical outcome, and look for association of specific organ involvement with risk factors., Methods: From January 2011 to October 2017, retrospective analysis of imaging investigations of 189 consecutive patients with culture-proven melioidosis was performed. Clinical and demographic records were collected from the hospital medical records., Results: Out of 67% with a localised disease musculoskeletal involvement was most common, whereas the common organs involved in disseminated infections were the lungs, spleen, liver and genitourinary tract in descending order. Twenty percent suffered unfavourable outcome with a mortality rate of 8.5%. The lung involvement was associated with unfavourable outcome (OR 3.2 [95%CI 1.54-6.63] p = 0.002). The lymph node involvement (OR 0.22 [95% CI 0.05-0.95] p = 0.04) predicted a favourable outcome. Those with diabetes were at a higher risk of splenic (OR 3.05 [95% CI 1.62-5.77]; p = 0.001) and musculoskeletal involvement (OR 2.14 [95% CI 1.09-4.17] p = 0.03) of melioidosis., Conclusions: In this study, we have described the spectrum of imaging manifestation of melioidosis and evaluated its association with clinical outcome. Respiratory system involvement in melioidosis showed significant association with unfavourable outcome. Diabetes mellitus, a common risk factor for melioidosis, is more prone for infection of the spleen and musculoskeletal system. Thus awareness of imaging manifestations of melioidosis can complement microbiological diagnostic tests for accurate early diagnosis and management.