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B Background: b Bacterial pneumonia and other invasive bacterial diseases (IBDs) are leading causes of morbidity and mortality in under-five children globally. Towards understanding the trends in common etiologies of bacterial pneumonia/IBDs and serotype distribution of S. Pneumoniae in pre and post-vaccination scenario, a hospital based surveillance network was established in 2016. Common etiological agents include Streptococcus pneumoniae, Haemophilus influenzae type b (Hib) and Neisseria meningitidis. [Extracted from the article]

Further comparison on genome variation amongst a subset of 20 Indian isolates (Invasive vs Non-Invasive) identified seven putative virulence factors that and may contribute to increasing bacterial virulence and bloodstream infections. B Background: b Salmonella enterica serotypes have expanded their host range where some serovars can infect a wide range of hosts. Pangenome analysis of a total of 70 genomes identified 8050 total genes including 3500 core genes and 4550 dispensable genes. [Extracted from the article]

The prevalence of S. pneumoniae, its serotype distribution and antimicrobial susceptibility profile are presented. In view of documented high prevalence of S. pneumoniae in bacterial meningitis in children, we recommend expansion of PCV 13 coverage for possible dual benefit against childhood pneumonias and bacterial meningitis. B Background: b Streptococcus pneumoniae is an important cause for pneumonia, meningitis, bacteremia and sepsis among under-five children. [Extracted from the article]

Background: Pentavalent vaccine (a combination vaccine which protects against five killer diseases- diphtheria, pertussis, tetanus, hepatitis B and Haemophilus influenzae type B) is being introduced in various states of India as a part of Universal Immunization Programme. In this context it is critical to establish sentinel sites across India for surveillance of H.influenzae type B meningitis and use this opportunity also for surveillance of pneumococcal and meningococcal meningitis. Keeping this in mind a hospital-based sentinel surveillance network was established at 11 places across the country and this study reports the results of first three years of this surveillance program. Methods & Materials: This study was conducted in six states of India through 11 hospital based sentinel sites. Children aged one to 59 monthswhometwith standard case definitions were included in the study and their sterile biological specimens were processed for laboratory identification of bacterial pathogens. Further characterizations of bacterial pathogens were in study reference laboratory. Reference laboratory reconfirmed bacterial identify and further characterized the isolates to identify serotypes and antimicrobial susceptibility profile. Results: A total of 10202 cases were suspected for bacterial meningitis in study population. Laboratory confirmed incidence rates for S. pneumonia, H. influenza and N. meningitidis in this study is found to be around 3.80%, 1.26% and 0.24% respectively. S. pneumoniae appears to be the predominant pathogen among laboratory identified bacterial pathogens with 71.7%, followed with H.influenzae (23.8%) and N.meningitidis (4.4%). For S.pneumoniae, 15% of positive cases had serotype data, showing serotypes 19F, 6B, 14, 6A and 14 were the predominant serotypes in India. Conclusion: Invasive bacterial disease appears to be a major problem in Indian children with S.pneumoniae dominating and H.influenzae decreasing in the pathogens list. If pneumococcal conjugate vaccine-13 incorporated into Universal Immunization Programme, it can provide protection against 79% of serotypes responsible for Invasive pneumococcal diseases in India. However continued surveillance representing all parts of the country is necessary to understand the complete picture of Invasive bacterial diseases in India. [ABSTRACT FROM AUTHOR]

Plasmid mediated colistin resistance was absent; mutations in mgrB, phoP and phoQ were predominant cause of colistin resistance. Susceptible ST23 hvKp carried only the virulence plasmid while MDR ST23 isolates carried 6 plasmids with resistance genes apart from virulence plasmid. B Background: b Klebsiella pneumoniae (Kp) is a notorious pathogen with high rates of extensively drug resistant isolates across the globe. [Extracted from the article]

B Background: b Pertussis, also known as whooping cough, caused by Bordetella pertussis, is a highly contagious, vaccine-preventable respiratory disease causing neonatal morbidity and mortality worldwide. The present study investigated the diversity of clinical B. pertussis strains against vaccine reference strains of India at genome structural level. [Extracted from the article]

B Results: b A total of 431 diphtheria suspected samples [isolates (n=194); throat swabs (n=218); other samples (n=19)] were received. B Background: b Diphtheria is a vaccine preventable disease caused by C. diphtheriae. [Extracted from the article]

Recombination resulting in changes in and around the active site of the transpeptidase domain of the penicillin binding protein (PBP) is responsible for beta lactam resistance. Absence of major lactam resistance related PBP mutations reveals gradual expansion of ST 271 to ST320 with low level beta lactam resistance. B Background: b Among S. pneumoniae serogroup 19, serotype 19F is the major serotype associated with lactam resistance and invasive pneumococcal disease (IPD) in India. [Extracted from the article]

Background: Emergence and spread of carbapenem resistance in Psuedomonas aeruginosa is on the rise. Resistance mechanisms for carbapenems are of various types. The most common are carbapenemase production, loss of porins and over-expression of efflux pumps. Presence of each of these resistance mechanisms contributes to various phenotypes such as imipenem resistant but meropenem susceptible (IRMS), meropenem resistant but imipenem susceptible (MRIS) and resistant to both imipenem and meropenem (IRMR). This study was undertaken to investigate the resistance mechanisms responsible for these different phenotypes. Methods & Materials: A total of 50 carbapenem resistant isolates of P.aeruginosa were collected from blood and respiratory samples of patients with ventilator associated pneumonia and/or bacteremia. Of the fifty isolates, 8 were IRMS, 3 were MRIS and 39 were IRMR phenotypes. Carbapenemase genes such as blaSPM, blaIMP, blaVIM, blaNDM, blaKPC and blaOXA-48 were screened for all the 50 isolates. In addition, for 8 IRMS, sequencing of OprD was done to look for the presence of mutations and relative quantification was done to quantify the OprD transcripts. While for three MRIS, relative quantification of mexAB efflux pump was done to quantify the over expression. Results: Of the 50 isolates, carbapenem resistance due to carbapenemase enzymes was found to be only 22%, which was due to blaVIM (n=7), blaNDM (n=3) and blaOXA-48 (n=1). Among the 8 IRMS isolates, only one was a blaVIM producer and seven isolates harbored multiple mutations in oprD gene. In addition, quantification revealed that, down regulation of oprD gene transcripts were found in few isolates. While for MRIS isolates, mexAB pump was found to be over-expressed. Conclusion: From this study we found that, IRMS is primarily due to the mutations across various regions in the loops of OprD gene, MRIS is due to the over expression of mexAB efflux pumps and IRMR is due to carbapenemases. This study results confirms that, these phenotypes are due to the different resistance mechanisms. This study also emphasizes that preliminary disc diffusion should be performed for both imipenem and meropenem particularly for P.aeruginosa, rather than testing single agents, as the resistance mechanisms for each of the agents are different. [ABSTRACT FROM AUTHOR]

Background: Melioidosis, caused by Burkholderia pseudomallei, is endemic to India and has been associated with significant morbidity and mortality. Since it mimics several other diseases, it is grossly under-recognised. This study was undertaken to describe the clinical manifestations, drugsusceptibility and outcomes of melioidosis in India. Methods & Materials: We carried out a retrospective study of adult patients admitted with culture proven melioidosis ina tertiary care hospital in South India from 2008 to 2014. Results: 114 patients, with a mean age of 45 years (92% males) were included. The patients were from 15 states, majority being from West Bengal (26.3%), Jharkhand (22.8%) and Tamil Nadu (14.9%). Common risk factors included diabetes (82.3%), and alcoholism (14%). The mean duration of symptoms, commonly fever, was 4 months and majority (78%) had multifocal disease. Patients presented in the cooler months (80.5%), especially in the acute group. Chronic melioidosis was commoner than acute disease (64% vs 36%). 11 patients (15%) among chronic melioidosis presented with an acute worsening and bacteremia. Bacteremia (80% vs 41%) and respiratory involvement (39% vs 16%) were more common in acute disease. Chronic granulomatous disease was associated with splenic (50% vs 29%), genitourinary (17.8 vs 4.9%) and bone involvement (12.3 vs 7%). Drug susceptibility to Carbepenems was 100%, Ceftazidime 98.1% while resistance to Trimethoprim-Sulfamethoxazole and Doxycycline was 5.9% and 2.6%. Our patients received induction therapy with Ceftazidime or Meropenem followed by eradication treatment with Trimethoprim-Sulfamethoxazole and Doxycycline. 50.9% patients required a surgical intervention and 21.9% were admitted to an intensive care unit. The case fatality rate was 14.9%. Bacteremia (p <0.001) and respiratory involvement (p=0.003) were associated with increased mortality. 57.9% patients were followed up and 3.5% patients had a relapse. Conclusion: Melioidosis is an emerging infection in India. Majority of the patients are diabetics presenting with chronic granulomatous disease. Patients with septicemia and respiratory involvement had poorer outcome. A high index of suspicion in the appropriate clinical setting, and early initiation of therapy are essential. [ABSTRACT FROM AUTHOR]

Background: Shigellae are the causative agents of bacillary dysentery, represents a significant public health problem worldwide especially in developing countries. New serotypes or subserotypes in Shigella are not uncommon and are reported from different parts of the world. Notably, atypical Shigella exhibit greater antibiotic resistance than typical Shigella serotypes and also found to harbour integrons which has the ability to acquire resistance genes. The purpose of this work was to amplify rfb regions (contains the genes coding for the enzymes responsible for O-antigen synthesis) of non-agglutinating Shigella isolates to characterize these by endonuclease restriction and to study the presence of antimicrobial resistance genes (AMR). Methods & Materials: A total of 3647 faeces specimens were processed between January to December 2014, among these, 27.5% (n = 176) were identified as Shigella spp. Eight non-agglutinable Shigella isolates obtained were included in the study for molecular characterization. These strains were tested for their antimicrobial susceptibility against six antibiotics by Kirby Bauer disc diffusion method. All the isolates were screened for the AMR genes (dhfr1A, sulII, bla-OXA, bla-TEM, bla-CTX-M, AmpC and qnrA,B,S) by PCR. The isolates were also amplified for their O-antigen gene cluster using Expand long template PCR system and the amplicons were further restricted using MboII enzyme. Results: The prevalence of shigellosis during the study period was 4.8%. The antimicrobial resistance for the atypical Shigella were 50% for ampicillin, co-trimoxazole (87%), nalidixic acid (37%), cefixime (12.5%) and all were susceptible to norfloxacin and cefotaxime. The AMR gene PCR results showed 25% of dhfr1A (n = 2), 62.5% sulII (n = 5), 50% bla-TEM (n = 4), 50% qnrS (n = 4) and all the isolates were negative for bla-OXA, bla-CTX-M and AmpC genes. rfb- RFLP results showed clearly identifiable and reproducible pattern, six different patterns were obtained. Conclusion: This study revealed the description of O-specific patterns allowing serotype identification without the use of antisera. Although the number of atypical Shigella strains in this study was only eight, thorough and strict monitoring of isolation of such atypical strains would help to understand the actual disease burden caused by the new Shigella serovars and consequently to study the epidemiology of shigellosis. [ABSTRACT FROM AUTHOR]

An emerging pathotype of Klebsiella pneumoniae, initially identified in Southeast Asian countries, has now spread to multiple countries, including India. These convergent strains, carrying both resistance and virulence determinants, are classified as multidrug-resistant Hypervirulent Klebsiella pneumoniae (MDR-HvKp). Since the initial reports, there has been a concerning surge in infections caused by this pathotype globally. In this context, we aim to shed light on the evolutionary changes that have taken place in this relatively novel pathotype. Understanding these changes is crucial for devising diagnosis and targeted intervention strategies to mitigate the spread of MDR-HvKp infections., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Introduction: The rising challenge of carbapenem-resistant Enterobacterales (CRE) infections in Indian healthcare settings calls for clear clinical guidance on the management of these infections. The Indian consensus on the management of CRE infection in critically ill patients (ICONIC-II) is a follow-up of the ICONIC-I study, which was undertaken in 2019., Areas Covered: A modified Delphi method was used to build expert consensus on CRE management in India, involving online surveys, face-to - face expert meetings, and a literature review. A panel of 12 experts was formed to develop potential clinical consensus statements (CCSs), which were rated through two survey rounds. The CCSs were finalized in a final face-to - face discussion. The finalized CCSs were categorized as consensus, near consensus, and no consensus., Expert Opinion: The outcomes included 46 CCSs (consensus: 40; near consensus: 3; and no consensus: 3). The expert panel discussed and achieved consensus on various strategies for managing CRE infections, emphasizing the significance of existing and emerging resistance mechanisms, prompt and tailored empiric therapy, and use of combination therapies. The consensus statements based on the collective expertise of the panel can potentially assist clinicians in the management of CRE infections that lack high-level evidence.

Rationale and Objectives: ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) constitute a threat to humans worldwide. India is now the most populous country. The goal was to investigate the evolution of the rates of antimicrobial resistance in ESKAPE pathogens across India over the 2010-20 decade., Methods: The data (89 studies) were retrieved from the Medline PubMed repository using specific keywords., Results: The study of 20 177 ESKAPE isolates showed that A. baumannii isolates were the most represented (35.9%, n = 7238), followed by P. aeruginosa (25.3%, n = 5113), K. pneumoniae (19.5%, n = 3934), S. aureus (16.3%, n = 3286), E. faecium (2.6%, n = 517) and Enterobacter spp. (0.4%, n = 89). A notable increase in the resistance rates to antimicrobial agents occurred over the 2010-20 decade. The most important levels of resistance were observed in 2016-20 for A. baumannii (90% of resistance to the amoxicillin-clavulanate combination) and K. pneumoniae (81.6% of resistance to gentamycin). The rise in β-lactamase activities was correlated with an increase in the positivity of Gram-negative isolates for β-lactamase genes., Conclusions: This review highlighted that, in contrast to developed countries that kept resistance levels under control, a considerable increase in resistance to various classes of antibiotics occurred in ESKAPE pathogens in India over the 2010-2020 decade., (Copyright © 2024 Elsevier Ltd and International Society of Antimicrobial Chemotherapy. All rights reserved.)

Streptococcus pneumoniae is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected characteristics were determined for 402 invasive isolates collected from children <5 years of age during routine surveillance from 1991 to 2020. Overall, the prevalence and diversity of vaccine type (VT) and non-vaccine type (NVT) isolates did not significantly change post-uptake of PCV. Individually, serotype 1 and global pneumococcal sequence cluster (GPSC or strain lineage) 2 significantly decreased, whereas serotypes 6B, 9V and 19A and GPSCs 1, 6, 10 and 23 significantly increased in proportion post-uptake of PCV. Resistance determinants to penicillin, erythromycin, co-trimoxazole, fluoroquinolones and tetracycline, and multidrug resistance significantly increased in proportion post-uptake of PCV and especially among VT isolates. Co-trimoxazole resistance determinants were common pre- and post-uptake of PCV (85 and 93 %, respectively) and experienced the highest rates of recombination in the genome. Accessory gene frequencies were seen to be changing by small amounts across the frequency spectrum specifically among VT isolates, with the largest changes linked to antimicrobial resistance determinants. In summary, these results indicate that as of 2020 this pneumococcal population was not yet approaching a PCV-induced equilibrium and they highlight changes related to antimicrobial resistance. Augmenting PCV coverage and prudent use of antimicrobials are needed to counter invasive pneumococcal disease in this region.

Background & Objectives: Sepsis, including neonatal sepsis, remains a prevalent cause of morbidity and mortality in low- and middle-income countries such as India, representing 85 per cent of all sepsis-related deaths globally. Early diagnosis and timely initiation of treatment is challenging due to non-specific clinical manifestations and non-availability of rapid diagnostic tests. There is an urgent need for affordable diagnostics with fast turnaround time catering to the needs of end-users. Target product profiles (TPPs) have been found instrumental in developing 'fit-for-use' diagnostics, thus reducing the time taken to facilitate development and improving diagnosis. Hitherto, no such guidance or criteria has been defined for rapid diagnostics for sepsis/neonatal sepsis. We propose an innovative approach for developing the diagnostics for sepsis screening and diagnosis which can be utilized by diagnostic developers in the country., Methods: Thr@ee-round Delphi method, including two online surveys and one virtual consultation, was adopted to define criteria for minimum and optimum attributes of TPPs and build consensus on characteristics. Expert panel (n=23) included infectious disease physicians, public health specialists, clinical microbiologists, virologists, researchers/scientists and technology experts/innovators., Results: We present a three-component product profile for sepsis diagnosis, (i) screening with high sensitivity, (ii) detection of aetiological agent, and (iii) profiling of antimicrobial susceptibility/resistance, in adults and neonates with an option of testing different considerations. An agreement of >75 per cent was achieved for all TPP characteristics by Delphi. These TPPs are tailored to the Indian healthcare settings and can also be extrapolated to other resource-constraint and high-disease burden settings., Interpretation & Conclusions: Diagnostics developed using these TPPs will facilitate utilization of invested resources leading to development of the products that have potential to ease the economic burden on patient and save lives., Competing Interests: None

Purpose: The COVID-19 pandemic was unique in the history of outbreaks because of the massive scaling up of resources related to diagnostics, treatment modalities, and vaccines. To understand the impact of the pandemic among laboratory professionals, we aimed to conduct a survey to assess the improvement in the lab capacity post-covid in terms of infrastructure and accreditation status across various levels of hospitals and to determine the changes in the practice of infection control precautions during the pandemic., Methods: This was an anonymous, online-based survey (using 58 item questionnaire) conducted between July 09, 2021, and August 07, 2021. The survey targeted all EQAS registered diagnostic laboratories located in India., Results: The survey reached out to 1182 participants, out of which 721 (61%) laboratories completed the questionnaire. During pre-COVID times, only 39% (282/721) of the laboratories had an RT-PCR facility. Among these 721 labs, 514 used open system RT-PCR assay, 217 labs used Truenat assay, 188 labs used GeneXpert assay, 31 used Abbott ID Now and 350 labs performed rapid antigen tests. During the pandemic, 55.3% got NABL accreditation and 7.4% were in the process of applying for COVID-19 molecular testing. In this, 80.7% of the laboratories participated in the ICMR - COVID quality control assessment. It was estimated that 41.4% of the laboratory professionals were re-using N95 masks. Overall, the infection prevention and control practices varied across each laboratory and hospital., Conclusion: These survey findings helped us to understand the strength and efficiency of laboratories in India in setting up new assays during a crisis time. Based on our findings, we propose to connect this network in a sustained manner to efficiently utilize the existing platforms to adapt to future pandemics., Competing Interests: Conflicts of interest None., (Copyright © 2022 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Background: In 2017, more than half the cases of typhoid fever worldwide were projected to have occurred in India. In the absence of contemporary population-based data, it is unclear whether declining trends of hospitalization for typhoid in India reflect increased antibiotic treatment or a true reduction in infection., Methods: From 2017 through 2020, we conducted weekly surveillance for acute febrile illness and measured the incidence of typhoid fever (as confirmed on blood culture) in a prospective cohort of children between the ages of 6 months and 14 years at three urban sites and one rural site in India. At an additional urban site and five rural sites, we combined blood-culture testing of hospitalized patients who had a fever with survey data regarding health care use to estimate incidence in the community., Results: A total of 24,062 children who were enrolled in four cohorts contributed 46,959 child-years of observation. Among these children, 299 culture-confirmed typhoid cases were recorded, with an incidence per 100,000 child-years of 576 to 1173 cases in urban sites and 35 in rural Pune. The estimated incidence of typhoid fever from hospital surveillance ranged from 12 to 1622 cases per 100,000 child-years among children between the ages of 6 months and 14 years and from 108 to 970 cases per 100,000 person-years among those who were 15 years of age or older. Salmonella enterica serovar Paratyphi was isolated from 33 children, for an overall incidence of 68 cases per 100,000 child-years after adjustment for age., Conclusions: The incidence of typhoid fever in urban India remains high, with generally lower estimates of incidence in most rural areas. (Funded by the Bill and Melinda Gates Foundation; NSSEFI Clinical Trials Registry of India number, CTRI/2017/09/009719; ISRCTN registry number, ISRCTN72938224.)., (Copyright © 2023 Massachusetts Medical Society.)

Purpose: Invasive non-typhoidal Salmonella (iNTS) disease is an important cause of morbidity and mortality in African countries. However, the incidence in Indian subcontinent remains poorly documented. This study has assessed the incidence of iNTS in India with a perspective on its AMR profiles and serovar distribution for a period of 21 years from 2000 to 2020 from a tertiary care centre in South India., Methods: A total of 461 iNTS isolates were subjected to serotyping and antimicrobial susceptibility testing (AST). A subset of isolates was genotyped by multi locus sequence typing (MLST) and results were compared to serotyping to predict the accuracy., Results: Overall, 461 iNTS isolates were characterised mostly comprising of S. Typhimurium (49.2%) and S. Enteritidis (28.8%). Proportion of isolates resistant to first line antibiotics such as ampicillin, chloramphenicol and trimethoprim/sulphamethoxazole were 6.7%, 1.7% and 3.6% respectively. Isolates resistant to third generation cephalosporin are at a gradual rise while decreased susceptibility to quinolones was most common. The incidence of iNTS infection was maximum in the age group of &gt;15 years. MLST analysis showed discrepancies in assigning the serovars by serotyping as three S. Saintpaul were identified as S. Typhimurium., Conclusion: The clinical epidemiology, serovar distribution and antimicrobial susceptibility patterns of invasive Salmonella isolates from India suggest that there is only a small burden of iNTS disease. However the gradual emergence of AMR in iNTS isolates indicates serious risk for public health warranting the importance enhanced molecular surveillance., Competing Interests: Conflict of interest The authors declare that there is no potential conflict of interest., (Copyright © 2022 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Purpose: Stenotrophomonas maltophilia is an emerging multi-drug resistant pathogen increasingly isolated in India. This study aimed to identify patients from whom Stenotrophomonas maltophilia had been isolated and assess predictors of mortality in this population., Methods: This was a retrospective cohort study of hospitalized patients with a positive culture for S. maltophilia over a 3-year period. Clinical details and laboratory results were assessed from hospital records. Bivariate and multivariate analysis was used to identify risk factors for mortality., Results: One hundred and nineteen patients (mean age 48.6 years) were included in the study. Of these, 111 patients were hospitalized for at least 48 ​hours prior to culture and 98 were admitted in the intensive care unit. Bivariate analysis revealed multiple associations with mortality, including a background of renal, cardiac, autoimmune disease, recent carbapenam use and COVID-19 infection and increasing ventilatory requirement, lower PaO 2 /FiO 2 (P/F) ratio, vasopressor use, thrombocytopenia, and hypoalbuminemia at the time of positive isolate. Multivariate analysis showed that autoimmune disease [OR 27.38; 95% CI (1.39-540)], a P/F ratio of less than 300 [OR 7.58; 95% CI (1.52-37.9)], vasopressor requirement [OR 39.50; 95% CI (5.49-284)] and thrombocytopenia [OR 11.5; 95% CI (2.04-65.0)] were statistically significantly associated with increased mortality, while recent surgery and receipt of antibiotics [OR 0.16; 95% CI (0.03-0.8)] targeted against S. maltophilia were associated with decreased mortality., Conclusion: Stenotrophomonas maltophilia is primarily isolated in patients in the intensive care unit. In our study the need for vasopressors, autoimmune disease, lower P/F ratios and thrombocytopenia were associated with higher mortality. The association of targeted antibiotics with reduced mortality suggests that the pathogenic role of S. maltophilia should not be underestimated. This finding needs to be confirmed with larger, prospective studies., Competing Interests: Declaration of competing interest The author declare no conflicts of interest., (Copyright © 2021 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Introduction. Bacterial dysentery is one of the greatest causes of morbidity and mortality worldwide. Campylobacter spp. and diarrhoeagenic Escherichia coli (DEC) are recognised as the most common causes of bacterial enteritis in developing countries including India. Hypothesis/Gap statement. Rapid and accurate identification of dysentery causing organisms using molecular methods is essential for better disease management, epidemiology and outbreak investigations. Aim. In view of the limited information available on the dysentery causing agents like Campylobacter spp., enterohemorrhagic E. coli (EHEC)/enteropathogenic E. coli (EPEC) and enteroinvasive E. coli (EIEC)/ Shigella in India, this study was undertaken to investigate the presence of these pathogens in human and poultry stool samples by molecular methods. Methodology. In total, 400 human stool samples and 128 poultry samples were studied. Microaerophilic culture along with real-time multiplex PCR with the targets specific to the genus Campylobacter , Campylobacter jejuni , Campylobacter coli , EHEC, EPEC and EIEC/ Shigella was performed. Further species confirmation was done using MALDI-TOF MS. Results. On microaerophilic culture, C. coli was isolated in one human sample and two C. jejuni and one C. fetus in poultry samples. On PCR analysis, among human stool samples, typical EPEC (42%) was predominantly seen followed by Campylobacter spp. (19%) and EIEC/ Shigella (10%). In contrast, Campylobacter spp. (41%) was predominant in poultry samples, followed by typical EPEC (26%) and EIEC/ Shigella (9%). Poly-infections with Campylobacter spp. and DEC were also observed among both sources. Conclusion. The present study documented the increased prevalence of Campylobacter spp. in humans compared with the results of previous studies from India. Typical EPEC was found to be predominant in children less than 5 years of age in this study. The high prevalence of coinfections in the current study indicates that a multiple aetiology of diarrhoea is common in our settings.

Diphtheria is caused by a toxigenic bacterium Corynebacterium diphtheria which is being an emerging pathogen in India. Since diphtheria morbidity and mortality continues to be high in the country, the present study aimed to study the molecular epidemiology of C. diphtheriae strains from India. A total of 441 diphtheria suspected specimens collected as part of the surveillance programme between 2015 and 2020 were studied. All the isolates were confirmed as C. diphtheriae with standard biochemical tests, ELEK's test, and real-time PCR. Antimicrobial susceptibility testing for the subset of isolates showed intermediate susceptibility to penicillin and complete susceptible to erythromycin and cefotaxime. Isolates were characterized using multi locus sequence typing method. MLST analysis for the 216 C. diphtheriae isolates revealed major diversity among the sequence types. A total of 34 STs were assigned with majority of the isolates belonged to ST466 (30%). The second most common ST identified was ST405 that was present in 14% of the isolates. The international clone ST50 was also seen. The identified STs were grouped into 8 different clonal complexes (CC). The majority belongs to CC5 followed by CC466, CC574 and CC209, however a single non-toxigenic strain belongs to CC42. This epidemiological analysis revealed the emergence of novel STs and the clones with better dissemination properties. This study has also provided information on the circulating strains of C. diphtheriae among the different regions of India. The molecular data generated through surveillance system can be utilized for further actions in concern., Competing Interests: The authors declare that no competing interest exist.

Background: Systematic studies to estimate the disease burden of typhoid and paratyphoid in India are limited. Therefore, a multicenter study on the Surveillance of Enteric Fever in India was carried out to estimate the incidence, clinical presentation, and antimicrobial resistance (AMR) trend. The data presented here represent the national burden of AMR in Salmonella Typhi and Salmonella Paratyphi A., Methods: Antimicrobial susceptibility testing was performed for S. Typhi and S. Paratyphi A (n = 2373) isolates collected prospectively during a 2-year period from November 2017 to January 2020., Results: Of 2373 Salmonella isolates, 2032 (85.6%) were identified as S. Typhi and 341 (14.4%) were S. Paratyphi A. Approximately 2% of S. Typhi were multidrug-resistant (MDR), whereas all 341 (100%) of S. Paratyphi A isolates were sensitive to the first-line antimicrobials. Among 98% of ciprofloxacin nonsusceptible isolates, resistance (minimum inhibitory concentration [MIC] >0.5 µg/mL) was higher in S. Typhi (37%) compared with S. Paratyphi A (20%). Azithromycin susceptibility was 99.9% and 100% with a mean MIC of 4.98 μg/mL for S. Typhi and 7.39 μg/mL for S. Paratyphi A respectively. Ceftriaxone was the only agent that retained 100% susceptibility. Moreover, beta-lactam/beta-lactamase inhibitors showed potent in vitro activity against the study isolates., Conclusions: Data obtained from this systematic surveillance study confirms the declining trend of MDR Salmonella isolates from India. The higher prevalence of ciprofloxacin nonsusceptibility enforces to limit its use and adhere to the judicious usage of azithromycin and ceftriaxone for enteric fever management., (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.)

Background: Acute febrile illness in children is frequently treated with antibiotics. However, the inappropriate use of antibiotics has led to the emergence of multidrug-resistant pathogens., Methods: We measured use of antibiotics for fever in 4 pediatric cohorts that were part of the Surveillance for Enteric Fever in India (SEFI) network. In this network, 24 062 children were followed up weekly, capturing information on fever and other morbidity between October 2017 and December 2019., Results: An antibiotic was given in 27 183 of the 76 027 (35.8%) episodes of fever. The incidence of fever-related antibiotic use was 58.0 (95% confidence interval [CI], 57.2-58.6) per 100 child-years. The median time to initiation of antibiotics was 4 days, and in 65% of those who received an antibiotic it was initiated by the second day. Antibiotics were continued for <3 days in 24% of the episodes. Higher temperature, younger age, male sex, joint family, higher education, internet access, and availability of personal conveyance were associated with antibiotic treatment for fever., Conclusions: In developing countries where antibiotic use is not regulated, broad-spectrum antibiotics are initiated early, and often inappropriately, in febrile illness. Frequent and inappropriate use of antibiotics may increase risk of antimicrobial resistance., (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.)

Background: Following a relatively mild first wave of coronavirus disease 2019 (COVID-19) in India, a deadly second wave of the pandemic overwhelmed the healthcare system due to the emergence of fast-transmitting SARS-CoV-2 genetic variants. The emergence and spread of the B.1.617.2/Delta variant considered to be driving the devastating second wave of COVID-19 in India. Currently, the Delta variant has rapidly overtaken the previously circulating variants to become the dominant strain. Critical mutations in the spike/RBD region of these variants have raised serious concerns about the virus's increased transmissibility and decreased vaccine effectiveness. As a result, significant scientific and public concern has been expressed about the impact of virus variants on COVID-19 vaccines., Objectives: The purpose of this article is to provide an additional explanation in the context of the evolutionary trajectory of SARS-CoV-2 variants in India, the vaccine-induced immune response to the variants of concern (VOC), and various vaccine deployment strategies to rapidly increase population immunity., Content: Phylogenetic analysis of SARS-CoV-2 isolates circulating in India suggests the emergence and spread of B.1.617 variant. The immunogenicity of currently approved vaccines indicates that the majority of vaccines elicit an antibody response and some level of protection. According to current data, vaccines in the pre-fusion configuration (2p substitution) have an advantage in terms of nAb titer, but the duration of vaccine-induced immunity, as well as the role of T cells and memory B cells in protection, remain unknown. Since vaccine efficacy on virus variants is one of the major factors to be considered for achieving herd immunity, existing vaccines need to be improved or effective next-generation vaccines should be developed to cover the new variants of the virus., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Objective: To assess the preparedness of veterinary laboratories in India to participate in an integrated antimicrobial resistance surveillance network and to address gaps in provision identified., Methods: The Indian Council of Medical Research and the Indian Council of Agricultural Research collaborated: (i) to select eight nationally representative veterinary microbiology laboratories whose capacity for participating in an integrated antimicrobial resistance surveillance network would be assessed using a standardized tool; (ii) to identify gaps in provision from the assessment findings; and (iii) to develop a plan, and take the necessary steps to address these gaps in consultation with participating organizations., Findings: The main gaps in provision identified were: (i) a lack of dedicated funding for antimicrobial resistance surveillance; (ii) the absence of standard guidelines for antimicrobial susceptibility testing; (iii) a shortage of reference strains for testing and quality assurance; and (iv) the absence of mechanisms for sharing data. We addressed these gaps by creating a veterinary standard operating procedure for antimicrobial susceptibility testing, by carrying out a validation exercise to identify problems with implementing the procedure and by conducting capacity-building workshops for veterinary laboratories., Conclusion: Antimicrobial resistance surveillance networks depend on the availability of accurate, quality-controlled testing. The challenges identified in creating an integrated surveillance network for India can be overcome by developing a comprehensive plan for improving laboratory capacity in human, veterinary and environmental sectors that is supported by the necessary funds. The study's findings may provide guidance for other low- and middle-income countries planning to develop a similar network., ((c) 2021 The authors; licensee World Health Organization.)

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: 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 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 bla OXA48-like was exclusively carried by ColKP3, whereas bla 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 NDM 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.

Streptococcus pneumoniae is the major cause of childhood pneumonia and related deaths in India. Widespread use of erythromycin for the treatment of pneumonia has led to the emergence of erythromycin resistance. Despite this increase in erythromycin resistance, there are very little data on resistance determinants from India. Hence, we aimed to perform the molecular characterization of erythromycin-resistant invasive pneumococcal isolates in India. In this study, 250 erythromycin-resistant invasive isolates obtained from four Indian hospitals between 2014 and 2019 were included. The isolates were reconfirmed by standard CDC protocols, followed by detection of erm(B), mef(A/E) genes, and screening for mutations in 23S rRNA, ribosomal proteins L4 and L22. Among the 250 erythromycin-resistant isolates, 46% (n = 114) and 35% (n = 87) carried the mef(A/E) gene and erm(B) gene, respectively; both genes were present in 8% (n = 20) of the isolates and 12% (n = 29) of the studied strains did not bear any of them. The major mutations associated with erythromycin resistance in 23S rRNA, such as A2060C, A2061G, and C2613G, were absent. The predominant serotypes were 19F, 14, 23F, 6A, 6B, 19A, and 9V. The major clonal complexes were CC320, followed by CC230 and CC63. The predominant gene was mef(A/E), and most of the serotypes were PCV13 (54%). This study contributes to the baseline understanding of the erythromycin resistance determinants associated with the serotypes and sequence types (ST) of Indian invasive S. pneumoniae., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Introduction: A hospital-based sentinel surveillance network for bacterial meningitis was established in India to estimate the burden of bacterial meningitis, and the proportion of major vaccine-preventable causative organisms. This report summarises the findings of the surveillance conducted between March 2012, and September 2016 in eleven hospitals., Methods: We enrolled eligible children with bacterial meningitis in the age group of one to 59 months. CSF samples were collected and processed for biochemistry, culture, latex agglutination, and real-time PCR. Pneumococcal isolates were serotyped and tested for antimicrobial susceptibility., Results: Among 12 941 enrolled suspected meningitis cases, 586 (4.5%) were laboratory confirmed. S. pneumoniae (74.2%) was the most commonly detected pathogen, followed by H. influenzae (22.2%), and N. meningitidis (3.6%). Overall 58.1% of confirmed bacterial meningitis cases were children aged between one, and 11 months. H. influenzae meningitis cases had a high (12.3%) case fatality rate. The serotypes covered in PCV13 caused 72% pneumococcal infections, and the most common serotypes were 14 (18.3%), 6B (12.7%) and 19F (9.9%). Non-susceptibility to penicillin was 57%. Forty-five (43.7%) isolates exhibited multidrug resistance, of which 37 were PCV13 serotype isolates., Conclusions: The results are representative of the burden of bacterial meningitis among under-five children in India. The findings were useful in rolling out PCV in the National Immunization Program. The non-susceptibility to penicillin and multidrug resistance was an important observation. Timely expansion of PCV across India will significantly reduce the burden of antimicrobial resistance. Continued surveillance is needed to understand the trend after PCV expansion in India., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objectives: Linezolid resistance in Enterococcus faecium is emerging worldwide. In this study, we aimed to characterise two linezolid-resistant E. faecium isolates using whole-genome sequencing., Methods: Antimicrobial susceptibility testing was performed by the broth microdilution method. A hybrid assembly approach of IonTorrent and MinION sequencing reads was used to generate the complete genome of linezolid-resistant E. faecium isolates VB3025 and VB3240., Results: VB3025 and VB3240 had minimum inhibitory concentration (MICs) for linezolid of 1024 μg/mL and 512 μg/mL, respectively. In addition, VB3025 was found to be resistant to both vancomycin and teicoplanin, while VB3240 was susceptible to these antibiotics. A hybrid assembly approach was used to generate the complete genome of VB3025 and VB3240 isolates harbouring the optrA gene. Notably, VB3025 carried two copies of optrA (chromosomal and plasmid), while in VB3240 optrA was identified on the chromosome. Interestingly, the plasmid pVB3025&#95;2 co-carried the resistance gene clusters aph(3)-IIIa-sat4-ant(6)-Ia-ermB, the vanHAX operon and a copy of the optrA gene. Moreover, the optrA gene inserted into a Tn554 transposon carrying the ermA gene was identified in both VB3025 and VB3240 isolates. Furthermore, mutation analysis revealed the presence of a G2592T mutation in the 23S rRNA of both isolates., Conclusion: This is the first study reporting optrA-positive linezolid-resistant E. faecium from India. A novel plasmid co-carrying vancomycin and linezolid resistance determinants highlights the threat for potential dissemination., Competing Interests: Declaration of Competing Interest None declared., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The emergence of multi drug resistant clone CC320 serotype19F/19A and their capsular (cps) antigenic variants due to selective pressures such as vaccine had been reported worldwide. Hence, it is important to identify the prevalent clones, sequence types and cps variants of serotype 19F/19A in India, where PCV13 has been recently introduced. Multi-locus sequence typing (MLST) was performed for all (n = 21) invasive S. pneumoniae isolates of serotype 19A (n = 5) and 19F (n = 16) collected between the years 2012 and 2018 from children less than 5 years. The genome characterization by whole genome sequencing for the Sequence types (STs) 320 and 271(n = 7) were performed and compared with another six Indian WGSs of similar STs available from the GPS platform. The predominant STs in the serotype 19F/19A study isolates were of CC320: ST 320, 236 and 271, associated with PMEN clone Taiwan 19F -14. The WGSs of CC320 study isolates showed high genomic similarity to the Taiwan 19F -14 clone, and the penicillin binding protein (PBP) amino acid sequence similarity was 100% for PBP1A, 93% for PBP 2B and 2X. Whilst PBP comparison with other global MDR ST320 strains revealed that the ST320 clones in India are of low-level penicillin resistance. The presence of a few ST320/19A/19F invasive isolates with high similarity to the Taiwan clone suggests slow and gradual expansion of Taiwan 19F -14 associated CC320 clones in India. Since serotype 19F/19A is covered by PCV13 vaccine, the expansion of 19F/19A cones with non-PCV13 vaccine serotype in India should be monitored.

Diphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox + isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.

Penicillin-binding proteins are the primary targets for beta lactam drugs, which are main stay of treatment for Streptococcus pneumoniae . The emergence of increased penicillin resistance in meningeal isolates of S. pneumoniae in India is alarming. With this background, we aimed to analyze the pbp gene mutations of penicillin nonsusceptible pneumococcal (PNSP) isolates from within India and their association with international clones. A total of 32 PNSP invasive isolates with a penicillin minimal inhibitory concentrations (MIC) of ≥ 0.12 μg/mL were subjected to PCR and sequencing for multilocus sequence typing and the pbp genes ( pbp2b , pbp2x , and pbp1a ). The S. pneumoniae R6 susceptible strain was used as the reference for the comparison analyses. In the majority of the present study isolates, amino acid substitutions were only seen in one of the three active sites of one of the three pbp genes. Thus, pbp genes in the absence of the major substitutions usually associated with penicillin resistance combined with mosaicism in pbp1a resulted in a slight increase in the penicillin MIC to between 0.06 and 2.0 μg/mL, which according to meningeal break point denote resistance. Clonal analyses revealed that the emergence of PNSP in India is due to the gradual expansion of the resistant clones CC320, CC230, and CC63.

Background: Recent reports reveal the emergence of Escherichia coli isolates harbouring a novel resistance mechanism based on four-amino-acid inserts in PBP3. These organisms concomitantly expressed ESBLs or/and serine-/metallo-carbapenemases and were phenotypically detected by elevated aztreonam/avibactam MICs., Objectives: The in vitro activities of the investigational antibiotic cefepime/zidebactam and approved antibiotics (ceftazidime/avibactam, ceftolozane/tazobactam, imipenem/relebactam and others) were determined against E. coli isolates harbouring four-amino-acid inserts in PBP3., Methods: Whole-genome sequenced E. coli isolates (n = 89) collected from a large tertiary care hospital in Southern India (n = 64) and from 12 tertiary care hospitals located across India (n = 25) during 2016-18, showing aztreonam/avibactam MICs ≥1 mg/L (≥4 times the aztreonam epidemiological cut-off) were included in this study. The MICs of antibiotics were determined using the reference broth microdilution method., Results: Four-amino-acid inserts [YRIK (n = 30) and YRIN (n = 53)] were found in 83/89 isolates. Among 83 isolates, 65 carried carbapenemase genes [blaNDM (n = 39), blaOXA-48-like (n = 11) and blaNDM + blaOXA-48-like (n = 15)] and 18 isolates produced ESBLs/class C β-lactamases only. At least 16 unique STs were noted. Cefepime/zidebactam demonstrated potent activity, with all isolates inhibited at ≤1 mg/L. Comparator antibiotics including ceftazidime/avibactam and imipenem/relebactam showed limited activities., Conclusions: E. coli isolates concurrently harbouring four-amino-acid inserts in PBP3 and NDM are an emerging therapeutic challenge. Assisted by the PBP2-binding action of zidebactam, the cefepime/zidebactam combination overcomes both target modification (PBP3 insert)- and carbapenemase (NDM)-mediated resistance mechanisms in E. coli., (© The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Shigella is the second leading cause of bacterial diarrhea worldwide. Recently, Shigella sonnei seems to be replacing Shigella flexneri in low- and middle-income countries undergoing economic development. Despite this, studies focusing on these species at the genomic level remain largely unexplored. Here, we compared the genome sequences of S. flexneri and S. sonnei isolates from India with the publicly available genomes of global strains. Our analysis provides evidence for the long-term persistence of all phylogenetic groups (PGs) of S. flexneri and the recent dominance of the ciprofloxacin-resistant S. sonnei lineage in India. Within S. flexneri PGs, the majority of the study isolates belonged to PG3 within the predominance of serotype 2. For S. sonnei , the current pandemic involves globally distributed multidrug-resistant (MDR) clones that belong to Central Asia lineage III. The presence of such epidemiologically dominant lineages in association with stable antimicrobial resistance (AMR) determinants results in successful survival in the community. IMPORTANCE Shigella is the second leading cause of bacterial diarrhea worldwide. This has been categorized as a priority pathogen among enteric bacteria by the Global Antimicrobial Resistance Surveillance System (GLASS) of the World Health Organization (WHO). Recently, S. sonnei seems to be replacing S. flexneri in low- and middle-income countries undergoing economic development. Antimicrobial resistance in S. flexneri and S. sonnei is a growing international concern, specifically with the international dominance of the multidrug-resistant (MDR) lineage. Genomic studies focusing on S. flexneri in India remain largely unexplored. This study provides information on the introduction and expansion of drug-resistant S. sonnei strains in India for the first time by comparing the genome sequences of Shigella strains in India for the first time by comparing the genome sequences of S. flexneri isolates from India with the publicly available genomes of global strains. The study discusses the key differences between the two dominant species of S. sonnei isolates from India with the publicly available genomes of global strains. The study discusses the key differences between the two dominant species of Shigella at the genomic level to understand the evolutionary trends and genome dynamics of emerging and existing resistance clones. The present work demonstrates evidence for the long-term persistence of all PGs of S. flexneri lineage in India.S. sonnei lineage in India., (Copyright © 2020 Muthuirulandi Sethuvel et al.)

Background: Otitis media, a disease highly prevalent among children worldwide, manifests clinically in both acute and chronic forms. The manner and time at which chronicity develops among Indian children is unknown., Aim: To study the prevalence, manifestations and risk factors for otitis media in a birth cohort aged 8 years., Methods: A birth cohort of 107 babies was followed up at 8 years of age and ENT evaluation with nasopharyngeal swabbing for detecting Streptococcus pneumoniae and Hemophilus influenzae was performed., Results: The overall prevalence of otitis media was 14%, almost half the prevalence in the first 2 years of life. Eight children (7.5%) with congested, bulging eardrums and no systemic symptoms had asymptomatic acute otitis media. Another five (4.7%) children had otitis media with effusion and 2 (1.9%) had chronic suppurative otitis media. Although 10/15 (66.7%) children with otitis media had positive swabs at 8 years age, only 2 were pneumococcal vaccine (PCV-13) serotypes. Risk factor analysis showed that passive smoking was the only significant parameter associated with otitis media (p = 0.029). Nasopharyngeal swabbing showed that 51/105 (48.6%) children had positive swabs for S. pneumoniae and 5/105 (4.8%) for S.pneumoniae with non-type b H. influenzae. The ten most commonly encountered pneumococcal serotypes were 6A,4,8,16F,33B,35A,35B, 18C, 19F and 23B which together comprised 29 of the 56 (51.8%) isolates. PCV-13 serotypes formed 19/56 (33.9%) to 21/56 (37.5%) of all pneumococcal isolates. Of 6 children who had received PCV-13, 4 tested positive for S. pneumoniae at 8 years of age too. However, none were vaccine serotypes. Four of those with otitis media who had positive swabs had received no immunisation at all and 3 of them had vaccine serotypes, viz. 4, 6A and 18C respectively., Conclusion: Indian children continue to have a high prevalence of otitis media at 8 years age. More than 1/3 of nasopharyngeal isolates at this age are vaccine serotypes. Passive smoking is an important risk factor for childhood otitis media and may contribute to the development of chronicity of the disease., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Objectives: Escherichia coli is regarded as one of the most commonly isolated Gram-negative pathogens from bloodstream infections. Increasing antimicrobial resistance (AMR) among E. coli is a threat to disease management as well as further dissemination of AMR genes to other clinically important pathogens. Here we report the genome of a multidrug-resistant (MDR) E. coli (BA22372) from a bloodstream infection belonging to ST410 B4/H24RxC subtype from India., Methods: Genomic DNA of E. coli BA22372 was sequenced using Ion Torrent™ PGM™ and MinION™ sequencing. Hybrid genome assembly was performed using short and long reads from both methods to achieve accurate and complete genome data., Results: Here we report the genome of MDR E. coli BA22372 harbouring bla OXA-181 and bla CTX-M-15 in two individual plasmids, namely pOXA181&#95;22372 (IncX3) and pCTX-M-15&#95;22372 (IncF). The pCTX-M-15 plasmid is well known to co-harbour bla NDM-5 , which was not seen in the studied isolate here., Conclusion: To the best of our knowledge, this is the first report of B4/H24RxC MDR E. coli from India co-harbouring bla CTX-M-15 and bla OXA-181 along with other AMR genes. Information from this genome data revealed the possession of AMR genes in two individual plasmids and their potential for rapid dissemination. This isolate is of high health concern as it harbours a plasmid with replicatory mechanisms capable of acquiring bla NDM-5 , which is a great threat for rapid dissemination of AMR. This study enhances our understanding of the AMR mechanisms among different clones of E. coli., (Copyright © 2020 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: Levonadifloxacin (WCK 771; IV) and its prodrug alalevonadifloxacin (WCK 2349; oral) are benzoquinolizine fluoroquinolones, recently approved in India for the treatment of acute bacterial skin and skin structure infections with concurrent bacteraemia and diabetic foot infections. Ahead of its market launch, the present study aimed to assess the in vitro activity of levonadifloxacin against contemporary Staphylococcus aureus isolates collected from a large tertiary care hospital in India. Additionally, levonadifloxacin activity was tested against hVISA and Bengal Bay clone MRSA isolates., Methods: Non-duplicate S. aureus (n = 793) isolates collected at Christian Medical College hospital, Vellore, India during 2013-19 were included in the study. MRSA isolates were identified using a cefoxitin disc diffusion assay. MICs of levonadifloxacin and comparator antibiotics were determined using the broth microdilution method. Mutations in QRDRs were identified for selected levofloxacin-non-susceptible isolates. MLST profiling was undertaken to detect the Bengal Bay clone., Results: Among the 793 isolates, 441 (55.6%) were MRSA and 626 (78.9%) were non-susceptible to levofloxacin. Levonadifloxacin showed MIC50 and MIC90 values of 0.25 and 0.5 mg/L, respectively, for all S. aureus, which included hVISA and Bengal Bay clone MRSA. The potency of levonadifloxacin was 16 times superior compared with levofloxacin., Conclusions: The present study demonstrated potent activity of levonadifloxacin against contemporary S. aureus isolates, which included MRSA isolates, hVISA isolates, Bengal Bay clone isolates and a high proportion of quinolone-non-susceptible isolates. The potent activity of levonadifloxacin observed in this study supports its clinical use for the treatment of S. aureus infections., (© The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Linezolid resistance has increasingly been described in coagulase negative staphylococci (CoNS) in recent years. Here, we describe the molecular mechanism of linezolid resistance in Staphylococcus haemolyticus using whole genome sequencing. Three S. haemolyticus isolates (VB5326, VB19458, and VB840) carried G2576T mutation at the domain V of the 23S rRNA. In addition, VB5326 and VB19458 carried the cfr gene in the chromosome. The presence of cfr gene, in combination with G2576T mutation in 23S rRNA, resulted in a high linezolid Minimum inhibitory concentration (MIC) of > 256 µg/ml. Three mutations, including D471E, I527M, and S532N, in rpoB contributed to an increased rifampicin MIC of 32 µg/ml. Subsequent development of linezolid and rifampicin resistance in S. haemolyticus is worrisome and greatly limits clinical management.

Background: Aminoglycoside resistance is a growing challenge, and it is commonly mediated by the aminoglycoside-modifying enzymes (AMEs), followed by 16S rRNA methyl transferase. Plazomicin, a novel aminoglycoside agent approved by the Food and Drug Administration for complicated urinary tract infections is proven to overcome resistance mediated by AMEs but not due to 16S rRNA methyl transferase (16SRMTases). We undertook this study to predict the efficacy of plazomicin in India based on the antimicrobial resistance profile derived from whole-genome sequencing (WGS)., Methodology: A total of 386 clinical isolates of Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii subjected to WGS were screened for aminoglycoside-resistance mechanisms such as AMEs and 16SRMTases and its association with carbapenemases., Results: AMEs was present in all E. coli, A. baumannii and in 90% of K. pneumoniae. In addition, up to 47% of E. coli and 38% of K. pneumoniae co-carried 16SRMTases with AMEs genes. However, A. baumannii showed 87% of isolates co-harbouring 16SRMTase. bla NDM, bla Oxa-48-like and bla Oxa-23-like were the most predominant carbapenemases in E. coli, K. pneumoniae and A. baumannii, respectively. Notably, 48% of NDM-producing E. coli and 35% of Oxa-48-like producing K. pneumoniae were identified to co-harbour AMEs + RMTAses, where plazomicin may not be useful., Conclusion: Overall, 53%, 62% and 14% of carbapenemase-producing E. coli, K. pneumoniae and A. baumannii harbours only AMEs, indicating the role of plazomicin use. Plazomicin can be used both for ESBLs as "carbapenem-sparing agent" and carbapenemase producers as "colistin-sparing agent." For optimal use, it is essential to know the molecular epidemiology of resistance in a given geographical region where plazomicin empirical therapy is considered., Competing Interests: None

Objectives: Acinetobacter baumannii emerged as a major nosocomial pathogen responsible for infections. In this study, we report the molecular characterization, association of insertion sequences and sequence types of clinical isolates of carbapenem resistant A. baumannii., Materials and Methods: A total of 763 non-duplicate isolates of A. baumannii received from 8 centres across India during January 2014 to December 2017 were studied. Susceptibility testing was done by Kirby-Bauer method. PCR was performed for detection of extended spectrum β-lactamases, metallo β-lactamases, oxacillinases and ISAba1. Mapping PCR was performed to identify the position of ISAba1 with respect to bla OXA-23 like and bla OXA-51 like gene. MLST was performed to identify the sequence type. Whole genome sequencing was done to decipher the genetic arrangement of ISAba1 with bla OXA-23 like and with bla OXA-51 like., Results: All the isolates were resistant to imipenem and meropenem. bla OXA-23 like was the predominant carbapenemase. All isolates were positive for ISAba1. The common sequence types were ST848, ST451 and ST1305 which belongs to International clone II. Whole genome sequencing showed considerable variation in the insertion site location., Conclusions: In conclusion, high prevalence of bla OXA-23 like in A. baumannii and its association with ISAba1 and sequence types belonging to IC-II facilitates the successful dissemination of these extremely drug resistant strains., (Copyright © 2019. Published by Elsevier Ltd.)

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.)

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

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.

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.