Evolutionary trends of carbapenem-resistant and susceptible Acinetobacter baumannii isolates in a major tertiary care setting from North India.

Emergence of carbapenem-resistant A. baumannii (CRAB) is a global, ongoing healthcare concern. CRAB is among the topmost priority pathogens, with various studies focusing on its global population structure and resistant allelic profiles. However, carbapenem-susceptible A. baumannii (CSAB) isolates are often overlooked due to their sensitivity to beta-lactams, which can provide important insights into origin of CRAB lineages and isolates. In the present study, we report genomic investigation of CRAB and CSAB coexisting in Indian hospital setting. MLST based population structure and phylogenomics suggest they mainly follow distinct evolutionary routes forming two phylogroups. PG-I exclusively for a successful clone (ST2) of CRAB and PG-II comprises diversified CSAB isolates except PG3373, which is CRAB. Additionally, there are few CRAB isolates not belonging to PG-I and sharing clonal relationship with CSAB isolates indicating role of genome plasticity towards extensive drug resistance in the nosocomial environment. Further, genealogical analysis depicts prominent role of recombination in emergence and evolution of a major CRAB lineage. Further, CRAB isolates are enriched in resistomes as compared to CSAB isolates, which were encoded on the genomic island. Such comparative genomic insights will aid in our understanding and localized management of rapidly evolving pandrug resistant nosocomial pathogens.

Corrigendum: Molecular markers associated to two non-allelic genic male sterility genes in peppers (Capsicum annuum L.).

[This corrects the article DOI: 10.3389/fpls.2018.01343.].

Genomic features, antimicrobial susceptibility, and epidemiological insights into Burkholderia cenocepacia clonal complex 31 isolates from bloodstream infections in India.

Introduction: Burkholderia cepacia complex (Bcc) clonal complex (CC) 31, the predominant lineage causing devastating outbreaks globally, has been a growing concern of infections in non-cystic fibrosis (NCF) patients in India. B. cenocepacia is very challenging to treat owing to its virulence determinants and antibiotic resistance. Improving the management of these infections requires a better knowledge of their resistance patterns and mechanisms. Methods: Whole-genome sequences of 35 CC31 isolates obtained from patient samples, were analyzed against available 210 CC31 genomes in the NCBI database to glean details of resistance, virulence, mobile elements, and phylogenetic markers to study genomic diversity and evolution of CC31 lineage in India. Results: Genomic analysis revealed that 35 isolates belonging to CC31 were categorized into 11 sequence types (ST), of which five STs were reported exclusively from India. Phylogenetic analysis classified 245 CC31 isolates into eight distinct clades (I-VIII) and unveiled that NCF isolates are evolving independently from the global cystic fibrosis (CF) isolates forming a distinct clade. The detection rate of seven classes of antibiotic-related genes in 35 isolates was 35 (100%) for tetracyclines, aminoglycosides, and fluoroquinolones; 26 (74.2%) for sulphonamides and phenicols; 7 (20%) for beta-lactamases; and 1 (2.8%) for trimethoprim resistance genes. Additionally, 3 (8.5%) NCF isolates were resistant to disinfecting agents and antiseptics. Antimicrobial susceptibility testing revealed that majority of NCF isolates were resistant to chloramphenicol (77%) and levofloxacin (34%). NCF isolates have a comparable number of virulence genes to CF isolates. A well-studied pathogenicity island of B. cenocepacia, GI11 is present in ST628 and ST709 isolates from the Indian Bcc population. In contrast, genomic island GI15 (highly similar to the island found in B. pseudomallei strain EY1) is exclusively reported in ST839 and ST824 isolates from two different locations in India. Horizontal acquisition of lytic phage ST79 of pathogenic B. pseudomallei is demonstrated in ST628 isolates Bcc1463, Bcc29163, and BccR4654 amongst CC31 lineage. Discussion: The study reveals a high diversity of CC31 lineages among B. cenocepacia isolates from India. The extensive information from this study will facilitate the development of rapid diagnostic and novel therapeutic approaches to manage B. cenocepacia infections.

Taxonomic and Phylogenomic Assessment Identifies Phytopathogenicity Potential of Stenotrophomonas maltophilia Complex.

Stenotrophomonas maltophilia is a versatile bacterium found in plants, water, air, and even hospital settings. Deep taxono phylogenomics studies have revealed that S. maltophilia is a complex of several hidden species that are not differentiated using conventional approaches. In the last two decades, there have been increasing reports of S. maltophilia as a pathogen of diverse plants. Hence, proper taxonogenomic assessment of plant-pathogenic strains and species within the S. maltophilia complex (Smc) is required. In the present study, we formally propose a taxonomic amendment of Pseudomonas hibiscicola and P. beteli, reported as pathogens of Hibiscus rosa-sinensis and Betelvine (Piper betle) plants, respectively, as a misclassified member species of the Smc. Recently, a novel species of the genus, S. cyclobalanopsidis, was reported as a leaf spot pathogen of the oak tree genus Cyclobalanopsis. Interestingly, our investigation also revealed S. cyclobalanopsidis as another plant-pathogenic member species of the Smc lineage. In addition, we provide deep phylo-taxonogenomic evidence that S. maltophilia strain JZL8, reported as a plant pathogen, is a misclassified strain of S. geniculata, making it the fourth member species of the Smc harboring plant-pathogenic strains. Therefore, a proper taxonomic assessment of plant-pathogenic strains and species from the Smc is required for further systematic studies and management.

Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane.

The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.

Bacillus licheniformis MCC 2514 genome sequencing and functional annotation for providing genetic evidence for probiotic gut adhesion properties and its applicability as a bio-preservative agent.

Bacillus licheniformis is a well-known probiotic that can be found in a variety of foods. The strain Bacillus licheniformis MCC 2514 was previously characterized by our group for its bio-physiological capabilities establishing it as a promising probiotic, but information on the genetic evidence for its attributes was lacking. In the current study, whole genome analysis identified the underlying molecular determinants responsible for its probiotic potential. The circular genome of MCC 2514 was 4,230,480 bp with 46.2% GC content, 24 rRNA, and 83 tRNA genes. The pangenome analysis between B. licheniformis MCC 2514 and 12 other B. licheniformis strains revealed a pangenome of 6008 genes and core genome of 3775 genes. Genome mining revealed NRPS and bacteriocins producing gene clusters indicating its biocontrol properties. Several genes encoding carbohydrate degrading enzymes, which aid in proper food degradation in the intestine, were also observed. Stress tolerance, vitamin, and essential amino acids biosynthesis related genes were found, which are important characteristics of a probiotic strain. Additionally, vital genes responsible for gut adhesion and biofilm formation were observed in its genome. The bacterium has been shown to improve the shelf life of idli batter by preventing whey separation, CO2, and odour production while maintaining the pH of 3.96-4.29, especially at cold temperatures. It has significantly reduced coliform contamination at both room and low temperatures, demonstrating its bio-preservative ability, which is also corroborated by the presence of the NRPS and bacteriocin gene clusters in its genome. The present study helped to understand both, the ability of B. licheniformis MCC 2514 to adapt the intestinal gut environment and its probiotic functionality for food preservation.

Comparative genomics analysis of genus Leuconostoc resolves its taxonomy and elucidates its biotechnological importance.

Genus Leuconostoc consists of a diverse range of lactic acid bacteria (LAB) from dairy, food and environmental ecology. Even though the species of Leuconostoc are commercially significant, their taxonomy is largely based on old, low-resolution classical methods. Several taxonomic reclassifications in the past were inadequate for microbiologist and food industry professionals to demarcate any new strain of genus Leuconostoc. The current taxonomy of the genus is largely based on classical approaches, which are in utmost need of reinvestigation by whole genome-based approaches. In the present study, the taxono-phylogenomic analysis depicted sixteen species, including three novel genomospecies and several reshufflings across the species, namely, L. mesenteroides, L. pseudomesenteroides, L. gelidum and L. lactis. Genus-wide T3PKS, CAZymes, and vector plasmids supports its biotechnological potential. However, detection of the antibiotic resistance genes in such an important LAB genus raises concern over their utility in industry. Present, large-scale in-depth genome-based study can shed light on the genome dynamics of the member species, help to obtain a more robust taxonomy and elucidate its biotechnology importance.

Reclassification of Streptococcus ilei as a later heterotypic synonym of Streptococcus koreensis based on whole-genome sequence analysis.

The genus Streptococcus, a member of family Streptococcaceae, is known for its wide range of industrial, clinical and human relevance. Among the species of genus Streptococcus two members, namely Streptococcus koreensis and Streptococcus ilei, were isolated from subgingival dental plaque and human small intestinal fluid, respectively. The 16S rRNA gene sequence similarity of the type strains of these members shows a similarity of 99.87%. In this study, we performed a systematic study to clarify the taxonomic assignment of these two species. Genome similarity assessment based on whole-genome sequence information such as average nucleotide identity using orthoANI and fastANI, digital DNA-DNA hybridization value between S. koreensis and S. ilei were 96.31, 96.60, 86.4 and 97.63, respectively. All these genome similarity values clearly exceeded the species delineation cutoffs. Phylogenetic assessment using 16S rRNA gene and whole-genome information using PhyloPhlAn, which uses around 400 conserved genes across bacterial phyla, provides additional evidence for these members forming a monophyletic clade in the phylogenetic tree. Pan genome analysis suggests a very large core genome (n = 1374) and the presence of no unique gene between the genomes of S. koreensis and S. ilei. Additionally, we found highly syntenic genomes of type strains of these two species. Based on these evidences, we propose S. ilei should be reclassified as a later heterotypic synonym of S. koreensis.

Genome-based reclassification of Streptococcus ursoris as a later heterotypic synonym of Streptococcus ratti.

Among the species of genus Streptococcus two members namely Streptococcus ratti and Streptococcus ursoris were isolated from oral cavity of rat and bear, respectively. Type strain of these members shows a 16S rRNA gene sequence similarity of 98.9%. Based on systematic phylo-taxonogenomics investigations, we could deduce the taxonomic assignment of the members of these species. Genome similarity assessment among the type strain of these members using average nucleotide identity (orthoANI and fastANI), digital DNA-DNA hybridization and average amino acid identity (AAI) were 98.5, 98.3, 88, and 98.3% respectively. All these values exceed the species delineation cutoffs suggesting a unified species. Phylogenetic tree obtained using 16S rRNA gene sequence also indicates the monophyletic nature of the member strains. Such monophyletic taxonomic positioning of the strains was further complemented with the whole genome-based phylogenomic tree. Based on these evidences, we propose S. ursoris should be reclassified as a later heterotypic synonym of S. ratti.

Genomic data resource of type strains of genus Pseudoxanthomonas.

Genus Pseudoxanthomonas represents a relatively newly characterized group of gamma-proteobacterium of environmental origin. Species of the genus have very similar morphology to strains belonging to Xanthomonas, Xylella and Stenotrophomonas. However, the genome resource of this genus was largely unexplored. The species belonging to the genus are from a wide range of environmental sites including hydrocarbon polluted fields. Here, we have provided the whole genome sequence of all available type strains of the genus of Pseudoxanthomonas. In order to deduce the differences with closely related genera, we have employed the whole genome-based investigation of the type species of genus Pseudoxanthomonas.

Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant.

BACKGROUND: Emergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events. METHODS: We have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant. RESULTS: Whole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR). CONCLUSION: Delta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations.

Phylo-Taxonogenomics Supports Revision of Taxonomic Status of 20 Xanthomonas Pathovars to Xanthomonas citri.

Based on phylo-taxonogenomics criteria, we present amended descriptions for 20 pathovars to Xanthomonas citri. Incidentally, 18 were first reported from India. Seven out of twenty are classified as X. axonopodis, 12 out of 20 as X. campestris, and one as X. cissicola. In this study, we have generated genome sequence data of four pathovars, and the genomes of the remaining 16 were used from the published data. Comprehensive genome-based phylogenomic and taxonogenomic analyses reveal that all these pathovars belong to X. citri and need to reconcile their taxonomic status. This proposal will aid in systematic studies of a major species and its constitutent members that infect economically important plants.

Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study.

BACKGROUND: COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India. OBJECTIVE: Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2. METHODS: High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC_045512.2) as reference. RESULTS: Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241). CONCLUSION: Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic.

Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas.

Genus Xanthomonas is a group of phytopathogens that is phylogenetically related to Xylella, Stenotrophomonas, and Pseudoxanthomonas, having diverse lifestyles. Xylella is a lethal plant pathogen with a highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas clades. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan-genome analysis identified a set of unique genes associated with sub-lineages representing plant-associated Xanthomonas clade and nosocomial origin Stenotrophomonas clade. Overall, our study reveals the importance of reconciling classical phenotypic data and genomic findings in reconstituting the taxonomic status of these four genera. SIGNIFICANCE STATEMENT: Xylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. An insect vector transmits the pathogen to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is significantly reduced both in terms of size (2 Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5 Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria and comparative studies, we assert the need to unify Xanthomonas with its relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor variant lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.

Xanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from India.

We report three yellow-pigmented, Gram-negative, aerobic, rod-shaped, motile bacterial isolates designated as PPL1T, PPL2, and PPL3 from healthy basmati rice seeds. Phenotypic and 16S rRNA gene sequence analysis assigned these isolates to the genus Xanthomonas. The 16S rRNA showed a 99.59% similarity with X. sacchari CFBP 4641T, a sugarcane pathogen. Further, biochemical and fatty acid analysis revealed it to be closer to X. sacchari. Still, it differed from other species in general and known rice associated species such as X. oryzae (pathogenic) and X. maliensis (non-pathogenic) in particular. Interestingly, the isolatess in this study were isolated from healthy rice plants but are closely related to species that is pathogenic and isolated from diseased sugarcane. Accordingly, in planta studies revealed that PPL1T, PPL2, and PPL3 are non-pathogenic to rice plants upon leaf inoculation. Taxonogenomic studies based on orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values with type strains of Xanthomonas species were below the recommended threshold values for species delineation. Whole genome-based phylogenomic analysis revealed that these isolates formed a distinct monophyletic clade with X. sacchari CFBP 4641T as their closest neighbour. Further, pangenome analysis revealed PPL1T, PPL2, and PPL3 isolates to comprise NRPS cluster along with a large number of unique genes associated with the novel species. Based on polyphasic and genomic approaches, a novel lineage and species associated with healthy rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov. is PPL1T (JCM 33631T = CFBP 8688T = ICMP 23426T = MTCC 12491T) and PPL2 (JCM 33632 = CFBP 8689 = ICMP 23427 = MTCC 12492) and PPL3 (JCM 33633 = CFBP 8690 = ICMP 23428 = MTCC 12493) as other strains of the species.

Comparative genomics and physiological investigation supported safety, cold adaptation, efficient hydrolytic and plant growth-promoting potential of psychrotrophic Glutamicibacter arilaitensis LJH19, isolated from night-soil compost.

BACKGROUND: Night-soil compost (NSC) has traditionally been conserving water and a source of organic manure in northwestern Himalaya. Lately, this traditional method is declining due to modernization, its unhygienic conditions, and social apprehensions. Reduction in the age-old traditional practice has led to excessive chemical fertilizers and water shortage in the eco-sensitive region. In the current study, a bacterium has been analyzed for its safety, cold-adaptation, efficient degradation, and plant growth-promoting (PGP) attributes for its possible application as a safe bioinoculant in psychrotrophic bacterial consortia for improved night-soil composting. RESULTS: Glutamicibacter arilaitensis LJH19, a psychrotrophic bacterium, was isolated from the NSC of Lahaul valley in northwestern Himalaya. The strain exhibited amylase (186.76 ± 19.28 U/mg), cellulase (21.85 ± 0.7 U/mg), and xylanase (11.31 ± 0.51 U/mg) activities at 10 °C. Possessing efficient hydrolytic activities at low-temperature garners the capability of efficient composting to LJH19. Additionally, the strain possessed multiple PGP traits such as indole acetic acid production (166.11 ± 5.7 µg/ml), siderophore production (85.72 ± 1.06% psu), and phosphate solubilization (44.76 ± 1.5 µg/ml). Enhanced germination index and germination rate of pea seeds under the LJH19 inoculation further supported the bacterium's PGP potential. Whole-genome sequencing (3,602,821 bps) and genome mining endorsed the cold adaptation, degradation of polysaccharides, and PGP traits of LJH19. Biosynthetic gene clusters for type III polyketide synthase (PKS), terpene, and siderophore supplemented the endorsement of LJH19 as a potential PGP bacterium. Comparative genomics within the genus revealed 217 unique genes specific to hydrolytic and PGP activity. CONCLUSION: The physiological and genomic evidence promotes LJH19 as a potentially safe bio-inoculant to formulate psychrotrophic bacterial consortia for accelerated degradation and improved night-soil compost.

Physiological and genomic evidence supports the role of Serratia quinivorans PKL:12 as a biopriming agent for the biohardening of micropropagated Picrorhiza kurroa plantlets in cold regions.

The medicinal herb, Picrorhiza kurroa Royle ex Benth has become endangered because of indiscriminate over-harvesting. Although micropropagation has been attempted for mass propagation of the plant, survival of in vitro plantlets under green house/open field poses a major challenge. Biopriming of micropropagated plantlets with plant growth-promoting rhizobacteria (PGPR) are among the successful methods to combat this problem. Serratia quinivorans PKL:12 was the best-characterized PGPR from rhizospheric soil of P. kurroa as it increased the vegetative growth and survival of the micropropagated plantlets most effectively. Complete genome (5.29 Mb) predicted genes encoding proteins for cold adaptation and plant growth-promoting traits in PKL:12. Antibiotic and biosynthetic gene cluster prediction supported PKL:12 as a potential biocontrol agent. Comparative genomics revealed 226 unique genes with few genes associated with plant growth-promoting potential. Physiological and genomic evidence supports S. quinivorans PKL:12 as a potential agent for bio-hardening of micropropagated P. kurroa plantlets in cold regions.

Genomic insights into evolution of extensive drug resistance in Stenotrophomonas maltophilia complex.

We report first complete genomic investigation of extensive drug resistance (XDR) in a nosocomial Stenotrophomonas maltophilia complex strain that is resistant to mainstream drugs (trimethoprim/sulfamethoxazole and levofloxacin). Comprehensive genomic investigation revealed its exclusive fourteen dynamic regions and highly enriched resistome comprising of two sulfonamide resistance genes on two diverse super-integrons of chromosomal origin. In addition, both these integrons harbour array of antibiotic resistance and commonly used disinfectant's resistance genes linked to ISCR elements. Isolation of a novel XDR strain from Indian tertiary care unit belonging to novel ST with diverse array of resistance genes on ISCR linked super-integrons indicates extent and nature of selection pressure in hospitals. Since, repetitive elements have major role in their spread and due to limitations of draft genomes, there is an urgent need to employ complete genome-based investigation for tracking the emergence of XDR at global level and designing strategies of antimicrobial stewardship and disinfection. IMPORTANCE: Hospital settings in India have one of the highest usages of antimicrobials and a heavy patient load. We hereby report a novel clinical isolate of S. maltophilia complex with two super-integrons that harbour array of antimicrobial resistance genes along with biocide and heavy metal resistance genes. Further, the presence of ISCR type of transposable elements on both the integrons indicates their propensity to transfer resistome while their chromosomal origin suggests possibilities for further genomic/phenotypic complexities according to selection pressure. Such complex mobile cassettes in a novel strain is a potential threat to global health care. Hence, to understand the evolution of opportunistic nosocomial pathogen, there is an urgent need to employ cost-effective long read technologies to keep vigilance on novel and XDR pathogens in populous countries. There is also need for surveillance of the usage of disinfectants and other antimicrobials for environmental hygiene and linked/rapid co-evolution of XDR in nosocomial pathogens. Repositories: Complete genome sequence of Stenotrophomonas maltophilia SM866: CP031058.