Isolation of bacterial DNA followed by sequencing and differing cytokine response in peritoneal dialysis effluent help in identifying bacteria in culture negative peritonitis.

AIM: The treatment of peritoneal dialysis related culture negative peritonitis is empirical which increases the cost of therapy and moreover antibiotic resistance. We aimed the study to isolate bacterial DNA from PD effluent and indentify bacteria causing peritonitis in culture negative situations. We have also studied the cytokine response with different bacteria causing peritonitis. METHODS: We have isolated bacterial DNA from PD effluent of culture negative and culture positive peritonitis patients. Bacterial DNA was subjected to polymerase chain reaction using universal bacteria specific primers and subsequently to Gram type specific primers for the differentiation of the etiologic agents into Gram-positive and Gram-negative. The amplified products were sequenced and subjected to blast search to identify agent at genus/ species level. RESULTS: Of the 30 molecular method positive samples, 16 (53.33%) samples were positive for Gram-negative bacteria and 4 (13.33%) for Gram-positive, while the remaining10 (33.33%) were positive for both Gram-positive and Gram-negative bacteria. We have found organisms that usually do not grow on normal culture methods. TNF-α was significantly associated with Gram-positive peritonitis and regulatory cytokine IL-10 with Gram-negative peritonitis. CONCLUSIONS: The molecular techniques are helpful in detecting and identifying organisms from culture negative PD effluent.

The Era of Device Colonizers: Chryseobacterium indologenes Infections from a Tertiary Care Center in North India.

BACKGROUND: Chryseobacterium indologenes is a hospital environment contaminant and can cause healthcare-associated infections. METHODS: Patients with C. indologenes infections in a tertiary care center in North India for 6 months were evaluated for susceptibility patterns, comorbidities, mechanical devices, risk factors, and treatment outcomes. The organism was provisionally identified phenotypically, and identification was confirmed by the BD Phoenix automated microbiology system. Minimum inhibitory concentration values of antibiotic susceptibility were determined. RESULTS: A total of 12 isolates of C. indologenes were recovered from 11 patients. Five patients had C. indologenes bloodstream infection (BSI), one had ventilator-associated pneumonia (VAP), and one had both BSI and VAP. In four others, the organism was isolated from the catheterized urinary tract. All VAP and BSI patients were admitted to the Intensive Care Units and mechanically ventilated; all had central lines and history of colistin therapy during the past 15 days. The common underlying risk factors were diabetes, hypertension, and coronary artery disease. CONCLUSIONS: C. indologenes infections are increasing because of higher use of carbapenems and colistin, to which it is intrinsically resistant.

Matrix metalloproteinases-2 and -9 in Campylobacter jejuni-induced paralytic neuropathy resembling Guillain-Barré syndrome in chickens.

Inflammation in Guillain-Barré syndrome (GBS) is manifested by changes in matrix metalloproteinase (MMP) and pro-inflammatory cytokine expression. We investigated the expression of MMP-2, -9 and TNF-α and correlated it with pathological changes in sciatic nerve tissue from Campylobacter jejuni-induced chicken model for GBS. Campylobacter jejuni and placebo were fed to chickens and assessed for disease symptoms. Sciatic nerves were examined by histopathology and immunohistochemistry. Expressions of MMPs and TNF-α, were determined by real-time PCR, and activities of MMPs by zymography. Diarrhea developed in 73.3% chickens after infection and 60.0% of them developed GBS like neuropathy. Pathology in sciatic nerves showed perinodal and/or patchy demyelination, perivascular focal lymphocytic infiltration and myelin swelling on 10th- 20th post infection day (PID). MMP-2, -9 and TNF-α were up-regulated in progressive phase of the disease. Enhanced MMP-2, -9 and TNF-α production in progressive phase correlated with sciatic nerve pathology in C. jejuni-induced GBS chicken model.

Assessment of Doripenem, Meropenem, and Imipenem against Respiratory Isolates of Pseudomonas aeroginosa in a Tertiary Care Hospital of North India.

OBJECTIVE: Pseudomonas aeruginosa is one of the leading pathogen causing healthcare-associated infections, particularly in immunocompromised and critically ill patients. The development of carbapenem resistance in P. aeruginosa infections is worrisome. Data specifically comparing the susceptibility of the three available carbapenems are lacking in the Indian subcontinent. MATERIALS AND METHODS: We evaluated the minimum inhibitory concentrations (MICs) of the three commonly used carbapenems- imipenem, meropenem, and doripenem against, 435 P. aeruginosa isolates obtained from respiratory samples and compared their susceptibility patterns to determine the best possible carbapenem among those available that may be used in combination regimes. RESULTS: Overall, 222 (51.0%) of isolates were susceptible to doripenem followed by imipenem 206 (47.3%) and meropenem 195 (44.8%), respectively. Two hundred and sixty-two (60.23%) strains were intermediate or resistant to at least one carbapenem. The MIC90 of all three carbapenems was >32 µg/ml while the MIC50 of meropenem was 16 µg/ml which was higher than MIC50 of both imipenem (4 µg/ml) and doripenem (2 µg/ml). CONCLUSION: Our study revealed that doripenem exerted better in vitro activity against the tested bacteria compared to imipenem and meropenem, but the difference was not statistically significant.

Transforming growth factor beta 1 (TGF-ß1) modulates Epstein-Barr virus reactivation in absence of Helicobacter pylori infection in patients with gastric cancer.

BACKGROUND: Transforming growth factor-beta 1 (TGF-ß1), a multifunctional cytokine, acts as a key factor for Epstein-Barr virus (EBV) reactivation. We investigated the role of TGF-ß1 in latent and lytic stages of EBV in relation to Helicobacter pylori infection among patients with gastric cancer (GC) and peptic ulcer disease (PUD). METHOD: Gastric mucosal TGF-ß1 expression was determined in 95 EBV positive patients with gastroduodenal pathology [GC 40, PUD 19 and non-ulcer dyspepsia (NUD) 36] by quantitative real time PCR. Presence of H. pylori infection was diagnosed when either culture or any two of three tests (RUT, histopathology and specific ureA PCR) were positive. Serum level of TGF-ß1 was detected among 60 patients using ELISA. RESULTS: Mucosal TGF-ß1 mRNA expression was detected in 85 of 95 EBV positive patients and it was significantly higher in patients with GC (p=0.042). TGF-ß1 expression tended to be higher among H. pylori non-infected than infected patients (3.80±6.24 vs. 2.07±2.50, p=0.085). Both mRNA and serum level had significant association with lytic stage of EBV in absence of H. pylori infection when compared with its presence (5.21±4.00 vs. 2.29±2.89, p=0.040 and 842.00 [669.55] vs. 662.63 [628.76], p=0.049; respectively). CONCLUSION: TGF-ß1 expression was significantly associated with GC. TGF-ß1 was higher both at expression and translational levels in lytic EBV infection without H. pylori suggests that H. pylori infection might play important role in preventing EBV reactivation through attenuated TGF-ß1 expression. This might be a "wise host defense against EBV reactivation".

A cost-effective anaerobic culture method & its comparison with a standard method.

Twenty six anaerobes were recovered from 150 deep-seated abscess samples cultured by the proposed two-step combustion-modified candle-jar system and Anoxomat. The degree of growth and colony size were similar in both systems, except for Clostridium difficile. The modified candle-jar system was found to be a sensitive and cost-effective alternative that might be used in resource-limited settings.

RmtC and RmtF 16S rRNA Methyltransferase in NDM-1-Producing Pseudomonas aeruginosa.

We investigated 16S rRNA methyltransferases in 38 blaNDM-1-positive Pseudomonas aeruginosa isolates and found RmtC in 3 isolates, 1 of which also harbored RmtF. The isolates were clonally unrelated; rmtC and rmtF genes were located on a chromosome with the blaNDM-1 gene. Strategies are needed to limit the spread of such isolates.

Tumor necrosis factor-α and interleukin-1ß gene polymorphisms and risk of brain abscess in North Indian population.

OBJECTIVE: Brain abscess develops in response to a parenchymal infection with pyogenic bacteria. Tumor necrosis factor-α (TNF-α) and interleukin-1ß (IL-1ß) are the most crucial pro-inflammatory cytokines with both beneficial and destructive properties for the central nervous system. The present study evaluated the association of specific alleles/genotypes of TNF-α and IL-1ß with brain abscess. MATERIAL AND METHODS: A total of 90 brain abscess patients and 100 healthy controls were included in the study. Predisposing factors were identified in 56 (62.2%) patients with brain abscess. TNF-α (-308 G>A) and IL-1ß (-511 CA) and C allele in IL-1ß (-511 CA) and IL-1ß (-511 C

Association of tumour necrosis factor-α polymorphism in patients with end stage renal disease.

AIM: Cytokines play a critical role in the pathophysiology of end stage renal disease (ESRD). Tumour necrosis factor-a (TNF-α) is an important cytokine involved in initiation and progression of renal diseases. The present study evaluated the association of specific alleles/genotype of TNF-α with chronic renal failure (CRF) and ESRD. METHODS: A total of 30 CRF patients who were not on renal replacement therapy, 85 ESRD patients and 120 healthy controls were included in the study. The ESRD patients belonged to two subgroups: patients on peritoneal dialysis (PD) without peritonitis (n = 50) and with peritonitis (n = 35). TNF-α genotype (-308 G > A) was determined by polymerase chain reaction-restriction fragment length polymorphism. Level of TNF-α was detected in the sera of patients and healthy controls by enzyme linked immunosorbent assay (ELISA), and also in the dialysate of patients on PD. RESULTS: The genotypic distributions of TNF-α (-308 G > A) were significantly different between patients and controls. Homozygous A/A genotype had significant association with CRF and ESRD (P < 0.001, odds ratio [OR] = 25.02). Frequency of homozygous A/A genotype was significantly higher in all subgroups of patients than controls (CRF 40% vs control 2.5%, P = 0.001; PD 54% vs control 2.5%, P < 0.001 and PD with peritonitis 62.8% vs control 2.5%, P < 0.001). Patients with homozygous A/A genotype had significantly elevated levels of TNF-α in the sera of patients and in the dialysate of PD patients. CONCLUSIONS: Individuals with homozygous TNF-α (-308 G > A) polymorphisms has significant association with CRF and ESRD, and thus may be a predictor for development of the disease. Elevated TNF-α may be a contributory factor.

Role of cytokines and Toll-like receptors in the immunopathogenesis of Guillain-Barré syndrome.

Guillain-Barré syndrome (GBS) is an autoimmune disease of the peripheral nervous system, mostly triggered by an aberrant immune response to an infectious pathogen. Although several infections have been implicated in the pathogenesis of GBS, not all such infected individuals develop this disease. Moreover, infection with a single agent might also lead to different subtypes of GBS emphasizing the role of host factors in the development of GBS. The host factors regulate a broad range of inflammatory processes that are involved in the pathogenesis of autoimmune diseases including GBS. Evidences suggest that systemically and locally released cytokines and their involvement in immune-mediated demyelination and axonal damage of peripheral nerves are important in the pathogenesis of GBS. Toll-like receptors (TLRs) link innate and adaptive immunity through transcription of several proinflammatory cytokines. TLR genes may increase susceptibility to microbial infections; an attenuated immune response towards antigen and downregulation of cytokines occurs due to mutation in the gene. Herein, we discuss the crucial role of host factors such as cytokines and TLRs that activate the immune response and are involved in the pathogenesis of the disease.

Helicobacter pylori cagL amino acid polymorphisms and its association with gastroduodenal diseases.

CagL is a pilus protein of Helicobacter pylori that interacts with host cellular α5ß1 integrins through its arginine-glycine-aspartate (RGD) motif, guiding proper positioning of the T4SS and translocation of CagA. Deletion or sequence variations of cagL significantly diminished the ability of H. pylori to induce secretion of IL-8 by the host cell. Therefore, this study was undertaken to investigate the association of cagL and its amino acid sequence polymorphisms with gastric cancer (GC), peptic ulcer disease (PUD), and non-ulcer dyspepsia (NUD) as there are no such studies from India. In total, 200 adult patients (NUD 120, PUD 30, GC 50) who underwent an upper gastrointestinal endoscopy were enrolled. H. pylori infection was diagnosed by rapid urease test, culture, histopathology, and PCR. The collected isolates were screened for cagL genotype by PCR and assessed for amino acid sequence polymorphisms using sequence translation. The prevalence of H. pylori infection in study population was 52.5%. Most of the isolates were cagL genopositive (86.6%), and all had RGD motif in their amino acid sequences. D58 and K59 polymorphisms in cagL-genopositive strains were significantly higher in GC patients (P < 0.05). Combined D58K59 polymorphism was associated with higher risk of GC (3.8-fold) when compared to NUD. In conclusion, H. pylori cagL amino acid polymorphisms such as D58K59 are correlated with a higher risk of GC in the Indian population. Further studies are required to know the exact role of particular cagL amino acid polymorphisms in the pathogenicity of H. pylori infection.

Evaluation of ELISA, neck muscle, tongue and eyelid examinations for the diagnosis of swine cysticercosis in a highly endemic area of north India.

Swine cysticercosis is very common in the developing countries where pigs are raised. Undercooked measly pork consumption leads to taeniasis; Taenia carriers act as source of human and swine cysticercosis and neurocysticercosis. Diagnosis of swine cysticercosis is important to break the cycle of disease transmission. The present study compared the neck muscle, tongue and eye examinations, and serum ELISA with different preparations (crude lysate, cyst fluid, scolex and cyst wall antigens) of Taenia solium cyst for the diagnosis of swine cysticercosis. Total of 24 pigs initially identified by neck muscle, tongue and eyelid examinations were purchased from local slaughter house and subjected to MRI for confirmation of cysticercosis. Sera from 20 MRI confirmed infected pigs and 50 disease free controls were subjected to ELISA with T. solium cyst antigens. Neck muscle examination was 100% sensitive and 75% specific for the diagnosis of swine cysticercosis, whereas tongue and eye examinations were 70% and 25% sensitive, respectively. ELISA with crude lysate had 85% sensitivity and 98% specificity. ELISA with cyst fluid, scolex and cyst wall antigens showed 70%, 65%, and 45% sensitivity, respectively. The present study showed that neck muscle examination was highly sensitive but less specific, while ELISA with crude antigens had reasonable sensitivity and high specificity for diagnosis of swine cysticercosis. ELISA with crude lysate can be used as a screening tool for swine infection.

Characterisation of OXA-48-like carbapenemases in Escherichia coli and Klebsiella pneumoniae from North India.

The oxacillinase-48 (OXA-48)-like carbapenemases are class D ß-lactamases and increasingly reported in Enterobacterial species. The detection of these carbapenemases is challenging and little information is available on the epidemiology and plasmid characteristics of OXA-48-like carbapenemase producers. We detected the presence of OXA-48-like carbapenemases in 500 clinical isolates of Escherichia coli and Klebsiella pneumoniae, followed by detection of other carbapenemases, extended spectrum ß-lactamases (ESBLs) and 16S rRNA methyltransferases in OXA-48 producers. Clonal relatedness was studied using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Finally, plasmid characterisation was performed through conjugation experiment, S1-PFGE and Southern hybridisation. Around 40% of E. coli and K. pneumoniae isolates harboured OXA-48-like ß-lactamases. Two OXA-48 allele variants, OXA-232 and OXA-181 were detected in our study. OXA-48 producers co-harbored diverse drug-resistant genes belonging to other classes of carbapenemases, ESBLs and 16S rRNA methyltransferases. OXA-48-like carbapenemase producers exhibited high clonal diversity. Bla OXA-48 carrying plasmids were conjugative, untypable and their size was ~ 45 kb and ~ 104.5 kb in E. coli and K. pneumoniae respectively. In conclusion, OXA-48-like carbapenemases have emerged as major cause of carbapenem resistance in Enterobacteriaceae and probably still being under reported. Strict surveillance and adequate detection methods are needed to prevent the dissemination of OXA-48-like carbapenemases.

Analysis of p53, K-ras gene mutation & Helicobacter pylori infection in patients with gastric cancer & peptic ulcer disease at a tertiary care hospital in north India.

BACKGROUND & OBJECTIVES: Mutations in the oncogene and tumour suppressor genes play an important role in carcinogenesis. We investigated the association of p53 and K-ras gene mutation and Helicobacter pylori infection in patients with gastric cancer (GC) and peptic ulcer disease (PUD) attending a tertiary care hospital in north India. METHODS: In total, 348 adult patients [62 GC, 45 PUD and 241 non-ulcer dyspepsia (NUD)] who underwent an upper gastrointestinal endoscopy were enrolled. H. pylori infection was diagnosed by rapid urease test, culture, histopathology and PCR. Mutation in the exon 5-8 of p53 gene was analyzed by PCR-single stranded conformational polymorphism (SSCP) and confirmed by sequence analysis. K-ras gene codon 12 mutation was analyzed by PCR-based restriction fragment length polymorphism. RESULTS: Overall p53 gene mutation was found in 4.6 per cent of the study population, and its distribution in GC, PUD and NUD was 21, 4.4 and 0.4 per cent, respectively. p53 gene mutation was significantly higher in patients with GC than PUD (P<0.05) and NUD (P<0.001). No difference in p53 gene mutation was observed between H. pylori infected and non-infected individuals. K-ras gene mutation was absent in all the patients. INTERPRETATION & CONCLUSIONS: Our results show that p53 gene mutation may be associated with gastric carcinogenesis independent to H. pylori infection and absence of K-ras gene mutation questions its role in the pathogenesis of GC and PUD in Indian patients.

Localized outbreaks of Pseudomonas aeruginosa belonging to international high-risk clones in a south Indian hospital.

Introduction. Pseudomonas aeruginosa is now considered as a major bacterial pathogen associated with hospital infections. Frequently, multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa are being encountered. Unusual increase in the P. aeruginosa infections led to the suspicion of outbreaks in the urology ward and cardiothoracic and vascular surgery intensive care unit (CTVS-ICU).Hypothesis. We hypothesize that the localized outbreaks may have originated from environmental sources within the hospital premises. An alternative possibility is the transmission from a previously infected patient or hospital attendant. Understanding the drug-resistance profile and genome characteristics of these clinical samples would determine the likely source of infection and spread.Aim. To perform epidemiological and molecular investigations on the suspected outbreaks of P. aeruginosa in the study centre and identify potential sources of infection.Methodology. Fourteen drug-resistant P. aeruginosa isolated from patients of the urology ward, CTVS-ICU and tap waters collected during the suspected outbreaks were subjected to microbiological and genomic analysis. Comparative genome (CG) analysis of these 14 study genomes with 284 complete P. aeruginosa genomes was performed.Results. Multilocus sequence typing analysis revealed that the isolates belonged to five different sequence types (ST235, ST357, ST639, ST654 and ST1203) and clustered into three distinct groups while two CTVS-ICU isolates remained as singletons. Genome analysis distinguished that the outbreaks in the urology ward and CTVS-ICU are independent, epidemiologically unrelated to each other and with the tap-water isolates.Conclusion. This study highlights the presence of distinct, clonally unrelated, drug-resistant P. aeruginosa within a hospital setting. The genome analysis of the two localized outbreaks revealed their distinct genetic background and phylogenetically unrelated origin. Vigilant screening and effective implementation of infection control measures led to the successful containment of potential environmental reservoirs of P. aeruginosa within the premises.

Immune response to different fractions of Taenia solium cyst fluid antigens in patients with neurocysticercosis.

The immunopathogenesis of neurocysticercosis (NCC) largely remains unknown. We analyzed the immune response to different fractions of Taenia solium cyst fluid antigens in patients with NCC. Lymphocytes were separated from 48 patients with NCC-related active epilepsy and 30 healthy controls. T. solium (isolated from pig muscles) antigens (crude lysate, CL; cyst wall, CW and cyst fluid, CF) at 20 µg/well concentrations were used to stimulate the cells in a lymphocyte transformation test (LTT). Only CF antigen stimulated cell proliferation significantly greater than control (p<0.001), hence cyst fluid antigens were further studied. The CF antigens were electro-blotted on nitrocellulose membrane (NC), cut at 0.5 cm distance and particulate antigens were prepared. A total of 12 fractions, designated F1 to F12 according to molecular weight were tested in-vitro for LTT. After 72 h of stimulation by the different fractions, Th1 (IL-1ß, TNF-α, IL-2) and Th2 (IL-4, IL-10) cytokine responses were determined in culture supernatants by ELISA. Low molecular weight fractions F1 through F4 (Mol. wt.<25 kDa) were found to be potent inducers of cytokines. Fractions F1, F3 and F4 induced the production of Th1 (IL-1ß, TNF-α, IL-2), whereas F2 induced the production of Th2 (IL-4 and IL-10) cytokine. The study shows that the low molecular weight fractions of CF antigens are immuno-dominant. Most of these fractions (F1, F3, F4) induce strong Th1 immune response except F2 which induces Th2 response. Further studies are needed to identify the different antigens present in these fractions to determine the molecules responsible for the immune response.

Toll-like receptor 4 polymorphism and its association with symptomatic neurocysticercosis.

BACKGROUND: Symptoms and signs of neurocysticercosis (NCC) are nonspecific and depend upon several factors, including the host immune response to the parasite. Toll-like receptors (TLRs) play an important role in innate immunity. Susceptibility of humans to NCC in relation to TLR polymorphism is unknown. The present study examines TLR4 polymorphism in human NCC and its role in symptomatic disease. METHODS: A total of 140 patients with NCC (82 symptomatic [ie, with active epilepsy] and 58 asymptomatic) and 150 healthy control subjects were examined for TLR4 Asp299Gly and Thr399Ile polymorphisms by means of polymerase chain reaction and restriction fragment-length polymorphism. RESULTS: TLR4 Asp299Gly and Thr399Ile were significantly associated with the occurrence of NCC (P < .001 for Asp299Gly; P = .003 for Thr399Ile) and progression to symptomatic NCC, compared with control subjects (P < .001 for Asp299Gly; P < .001 for Thr399Ile) or asymptomatic NCC (P < .001 for Asp299Gly; P = .002 for Thr399Ile). Frequency of haplotype Gly/Thr (P <.001) was observed to be a risk factor for susceptibility to NCC. Gly and Ile carriers had a statistically significant association with NCC (P < .001 for Gly; P = .003 for Ile) and symptomatic NCC (P < .001 for Gly; P

My experience on taeniasis and neurocysticercosis.

Taeniasis and neurocysticercosis (NCC) are major public health problems in developing countries. NCC is the leading cause of community-acquired active epilepsy. NCC may present as a medical emergency, especially when there is cysticercotic encephalitis or raised intracranial hypertension. Systematic community-based studies on taeniasis and NCC are lacking. We studied taeniasis and NCC-related active epilepsy disease burden in the pig farming community of Lucknow district, Uttar Pradesh, India. Based on the 30 cluster sampling approach as recommended by the World Health Organization, we estimated the prevalence of taeniasis, NCC-related active epilepsy, and silent NCC in the community. We also estimated the prevalence of swine cysticercosis. Taeniasis was detected in 18.6% of populations. Expulsions of tapeworm segments in stool, consumption of undercooked pork, age above 15 years, and handwash with clay or plain water after defecation were associated with taeniasis. On molecular analyses of positive stool samples, T. solium was identified in 40% and Taenia asiatica in 60% of cases. Active epilepsy was identified in 5.8% of subjects; 48% of them had NCC. On neuroimaging, NCC was detected in 15% of asymptomatic individuals. We observed that host genetic factors such as toll-like receptor-4, matrix metalloproteinase-9, intercellular adhesion molecule-1, and glutathione-S transferase gene polymorphisms were associated with seizure in NCC. When peripheral blood mononuclear cells (PBMCs) from NCC subjects were exposed to cysticerci fluid antigens in-vitro, PBMCs from symptomatic and asymptomatic subjects showed significantly higher Th 1 and Th 2 cytokines response respectively, symptomatic patients had significant Th-1 cytokines response, while asymptomatic individuals showed Th-2 response. Porcine cysticercosis was detected in 26% of swine; 38% of them had cysticerci in the brain. Swine with brain involvement showed clinical signs such as excessive salivation, excessive blinking and tearing, and subconjunctival nodule. On molecular analysis, 15% of cysticerci in swine were identified as T. asiatica. Infected swine when treated with albendazole plus/minus steroid, the response rate of cysticerci (either dead or resolved lesion) was 100% in albendazole-treated group and 71% in albendazole plus steroid-treated group. The above studies suggest that taeniasis and NCC are alarmingly high in the pig farming community of North India. Taeniasis in human and cysticercosis in swine due to T. asiatica call for further studies on this parasite.

Genetic Characterisation of Colistin Resistant Klebsiella pneumoniae Clinical Isolates From North India.

Background: Increasing use of colistin has led to the world-wide emergence of mobile colistin resistant gene (mcr). The present study aimed to identify and characterise mcr and other drug-resistant genes in colistin resistant Klebsiella pneumoniae clinical isolates. Methods: Twenty-two colistin resistant K. pneumoniae were analysed for mcr and other drug-resistant genes, efflux pumps, and virulence genes, and for their biofilm forming ability. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were performed for all mcr-1 positive isolates. S1-PFGE and Southern hybridisation were performed for localisation of mcr-1 and blaNDM. Results: Nineteen colistin resistant K. pneumoniae harboured mcr-1 and 3 had mgrB disruption. All isolates harboured blaOXA-48-type and ESBL genes; eight strains (five with mcr-1 and three with mgrB disruption) co-harboured blaNDM. Efflux pumps genes AcrAB and mdtK were detected in all 22 and tol-C in 21 isolates. Virulence-related genes entB and irp-1 were detected in all 22, mrkD in 20, and fimH-1 in 18 isolates; 11 isolates were strong biofilm producers. PFGE clustered mcr-1 positive isolates into eight groups based on ≥90% similarity; MLST revealed diverse sequence types, predominant being ST-15 (n = 4) and ST-16 (n = 4). Both mcr-1 and blaNDM were localised on plasmid and chromosome; mcr-1 was present on IncFII type and blaNDM on IncFIB and IncA/C type plasmids. Conclusions: Colistin resistance in K. pneumoniae was predominantly mediated by mcr-1. Co-existence of colistin, carbapenem, and other drug-resistant genes along with efflux pumps indicates towards enormous genomic plasticity in K. pneumoniae with ability to emerge as super-spreader of drug-resistance.

Complete genome sequence of an extensively drug-resistant Pseudomonas aeruginosa ST773 clinical isolate from North India.

OBJECTIVES: Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen causing a wide range of community- and hospital-acquired infections. Here we report the complete genome sequence of an extensively drug-resistant (XDR) P. aeruginosa strain (PA790) in order to understand the antibiotic resistance genes (ARGs) harboured by such a strain. METHODS: Whole-genome sequencing (WGS) was performed using Illumina HiSeq and Nanopore MinION platforms. Genome assembly was performed using Unicycler v.0.4.8. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). In silico predictions were fulfilled using curated bioinformatics tools. RESULTS: Pseudomonas aeruginosa PA790 was classified as XDR and belongs to sequence type 773 (ST773). The complete genome size is 6 932 250 bp with a G+C content of 66.02% and a BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 100. Strain PA790 harboured 12 different ARGs conferring resistance to eight different classes of antibiotics. It was identified as the nineteenth ST773 strain among 5785 whole-genome sequences of P. aeruginosa available in the NCBI database. CONCLUSION: Pseudomonas aeruginosa PA790 belongs to ST773 and was identified as the nineteenth such isolate to be submitted to NCBI and the first complete ST773 genome from India. The WGS data with multiple ARGs of P. aeruginosa PA790 (ST773) will aid in understanding the evolution and phylogeny of such high-risk clones and provide a solid basis for further research on XDR strains.