Biocide-Resistant Escherichia coli ST540 Co-Harboring ESBL, dfrA14 Confers QnrS-Dependent Plasmid-Mediated Quinolone Resistance.

Emerging sequence types of pathogenic bacteria have a dual ability to acquire resistance islands/determinants, and remain renitent towards disinfection practices; therefore, they are considered "critical risk factors" that contribute significantly to the global problem of antimicrobial resistance. Multidrug-resistant Escherichia coli was isolated, its genome sequenced, and its susceptibilities characterized, in order to understand the genetic basis of its antimicrobial resistance.The draft genome sequencing of E. coli ECU32, was performed with Illumina NextSeq 500, and annotated using a RAST server. The antibiotic resistome, genomic island, insertion sequences, and prophages were analyzed using bioinformatics tools. Subsequently, analyses including antibiotic susceptibility testing, E-test, bacterial growth, survival, and efflux inhibition assays were performed.The draft genome of E. coli ECU32 was 4.7 Mb in size, the contigs were 107, and the G+C content was 50.8%. The genome comprised 4658 genes, 4543 CDS, 4384 coding genes, 115 RNA genes, 88 tRNAs, and 3 CRISPR arrays. The resistome characterization of ST540 E. coli ECU32 revealed the presence of ESBL, APH(6)-Id, APH(3')-IIa, dfrA14, and QnrS1, with broad-spectrum multidrug and biocide resistance. Comparative genome sequence analysis revealed the presence of transporter and several virulence genes. Efflux activity and growth inhibition assays, which were performed with efflux substrates in the presence of inhibitor PAßN, exhibited significant reduced growth relative to its control.This study discusses the genotypic and phenotypic characterization of the biocide-tolerant multidrug-resistant E. coli O9:H30 strain, highlighting the contributory role of qnrS-dependent plasmid-mediated quinolone resistance, in addition to innate enzymatic modes of multidrug resistance mechanisms.

Genotypic and Phenotypic Characterization of Novel Sequence Types of Carbapenem-Resistant Acinetobacter baumannii, With Heterogeneous Resistance Determinants and Targeted Variations in Efflux Operons.

Acinetobacter baumannii has emerged as one of the dominant nosocomial human pathogens associated with high morbidity and mortality globally. Increased incidences of carbapenem-resistant A. baumannii (CRAB) have resulted in an enormous socioeconomic burden on health-care systems. Here, we report the genotypic and phenotypic characterization of novel ST1816 and ST128 variants in A. baumannii strains belonging to International clone II (GC2) with capsule types KL1:OCL8 and KL3:OCL1d from India. Sequence analysis revealed the presence of diverse virulome and resistome in these clinical strains, in addition to islands, prophages, and resistance genes. The oxacillinase bla OXA-23 detected in the genomic island also highlighted the coexistence of bla OXA-66 /bla OXA-98 , bla ADC73 /bla ADC-3 , and bla TEM-1D in their mobile scaffolds, which is alarming. Together with these resistance-determining enzymes, multidrug efflux transporters also harbored substitutions, with increased expression in CRAB strains. The hotspot mutations in colistin resistance-conferring operons, PmrAB, LpxACD, and AdeRS, were additionally confirmed. Phenotype microarray analysis indicated that multidrug-resistant strains A. baumannii DR2 and A. baumannii AB067 preferred a range of antimicrobial compounds as their substrates relative to the other. To our knowledge, this is the first comprehensive report on the characterization of A. baumannii variants ST1816 and ST128, with different genetic makeup and genome organization. The occurrence of CRAB infections worldwide is a severe threat to available limited therapeutic options; hence, continued surveillance to monitor the emergence and dissemination of such novel ST variants in A. baumannii is imperative.

Comparative genome analysis and characterization of a MDR Klebsiella variicola.

Klebsiella variicola is an emerging pathogen responsible for causing blood-stream infections, urinary and respiratory tract related diseases in humans. In this report, we describe the genome sequence data and phenotypic characterization of K. variicola strain KV093 isolated from India. Comparative genome sequence analysis revealed the presence of genes linked with virulence, iron acquisition and transport, type 1 and type 3 pili, secretion systems including the capsular gene cluster. The plant-associated genes such as nitrogen fixation, growth and defense mechanisms against oxidative stress were also identified. On performing antibiotic susceptibility testing, growth inhibition, and stress challenge assays it was observed that the drug resistant K. variicola KV093 exhibited cross resistance to various antibiotics, antiseptics, including disinfectants. This report highlights the arsenal of virulence and antibiotic resistance determinants in K. variicola KV093, an effort emphasizing the current pressing need for regular surveillance of K. variicola strains especially in India.

A cross-sectional study of stool form (using Bristol stool chart) in an urban South Indian population.

BACKGROUND: There is paucity of data on Bristol stool form (BSF) in healthy South Indian residents. AIM: To determine the BSF types and associated factors in an urban bowel health noncomplainant population. METHODS: This cross-sectional study, performed using a self-administered questionnaire among adult Chennai residents, compared BSF types by gender for various factors (age, occupation, bowel frequency, and defecation-related abdominal pain). BSF types 1/2 and 6/7 were grouped as hard and loose stools, respectively. The statistical tests used were proportion test, χ 2, and Kruskal-Wallis tests (P < 0.05 deemed significant). RESULTS: The study cohort of 1402 subjects included 748 (53.3%) men and a third each of professionals, semiprofessionals, and "non-office goers" (homemakers, retirees, students, and unemployed). A total of 97% had daily bowel movement, and 8.5% reported defecation associated abdominal pain. The BSF types in decreasing prevalence were: Type 3 (35.6%), Type 4 (32.5%), Types 1 or 2 (20.5%), Type 5 (6.9%), and Types 6 or 7 (4.5%). On gender comparison, significantly more men passed hard (P = 0.03) or loose stools (P = 0.001), while more women passed Type 3 (P = 0.0002). Loose stools in men were associated with abdominal pain (P = 0.0035). Women passing hard or loose stool types were slightly older (median age in 30s vs. 20s in Types 3-5) and had reduced stool frequency (P = 0.026: hard; P = 0.006: loose). CONCLUSIONS: This South Indian noncomplainant cohort's most common stool types were BSF Types 3 and 4, with few gender variations in extreme stool types.

Genome analysis of urease positive Serratia marcescens, co-producing SRT-2 and AAC(6')-Ic with multidrug efflux pumps for antimicrobial resistance.

In this study, we present the genome sequence of Serratia marcescens SM03, recovered from a human gut in India. The final assembly consists of 26 scaffolds (4620 coding DNA sequences, 5.08 Mb, 59.6% G + C ratio) and 79 tRNA genes. Analysis identified novel genes associated with lactose utilization, virulence, P-loop GTPases involved in urease production, CFA/I fimbriae apparatus and Yersinia - type CRISPR proteins. Antibiotic susceptibility testing indicated drug tolerant phenotype and inhibition assays demonstrated involvement of extrusion in resistance. Presence of enzymes SRT-2, AAC(6')-Ic, with additional Ybh transporter and EamA-like efflux pumps signifies the genetic plasticity observed in S. marcescens SM03.

Genome sequence and comparative analysis of Bacillus cereus BC04, reveals genetic diversity and alterations for antimicrobial resistance.

In this study, we delineated the genome sequence of a Bacillus cereus strain BC04 isolated from a stool sample in India. The draft genome is 5.1 Mb in size and consists of total 109 scaffolds, GC content is 35.2% with 5182 coding genes. The comparative analysis with other completely sequenced genomes highlights the unique presence of genomic islands, hemolysin, capsular synthetic protein, modifying enzymes accC7 and catA15, regulators of antibiotic resistance MarR and LysR with annotated functions related to virulence, stress response, and antimicrobial resistance. Overall, this study not only signifies the genetic diversity in gut isolate BC04 in particular, but also pinpoints the presence of unique genes possessed by B. cereus which can be pertinently exploited to design novel drugs and intervention strategies for the treatment of food borne diseases.

Health-related quality of life in liver cirrhosis patients using SF-36 and CLDQ questionnaires.

AIM OF THE STUDY: To determine the factors that are likely to influence the domains of health-related quality of life (HRQOL) using SF-36 and CLDQ questionnaires in patients with liver cirrhosis. MATERIAL AND METHODS: Patients with liver cirrhosis were compared with age- and gender-matched healthy controls for physical and mental components of the SF-36 score. Effects of age, co-morbidity, namely diabetes, severity of liver disease and complications of liver cirrhosis on HRQOL using self-administered or by direct interview SF-36 and CLDQ questionnaires were studied. Statistical analysis: chi square test, ANOVA, Kruskal-Wallis test and stepwise linear regression analysis. A p value of < 0.05 was considered significant. RESULTS: Regarding SF-36 score, except for bodily pain, 149 patients had significantly low individual and composite domain scores (p value < 0.0001) compared to age/gender-matched controls. Patients below 45 years, the majority of whom belonged to Child-Turcotte-Pugh (CTP) class C with a high Model of End-Stage Liver Disease (MELD) and higher rates of complication had low SF-36 for bodily pain (KW p < 0.005) and those above 55 years for physical function (p < 0.05). Both the physical components had a major impact on mental composite score (MCS) (KW p < 0.05). The overall CLDQ score was also low in patients below 45 years old (p < 0.05). Diabetes with or without other co-morbid conditions had no effect on SF-36 or CLDQ scores, while non-diabetic co-morbid conditions did on physical domains (physical function, bodily pain and role physical) and the physical component score of SF-36 (KW p < 0.01 to < 0.0001). In linear regression, MELD had a direct and significant association with overall PCS, MCS and CLDQ. CONCLUSIONS: Age below 45 years, higher MELD and CTP score with the presence of ascites and hepatic encephalopathy affect the overall CLDQ scores.

Seroprevalence of cytomegalovirus in donors & opportunistic viral infections in liver transplant recipients.

BACKGROUND & OBJECTIVES: Opportunistic virus infections are common in liver transplant (LT) recipients. There is a risk of developing infection with cytomegalovirus (CMV) and herpes-related viruses such as herpes simplex virus-1 and 2 (HSV-1 & 2), Epstein-Barr virus (EBV) and Varicella Zoster virus (VZV), reactivation of infection and recurrent infection. This study was conducted to determine CMV seropositivity in donors and its influence on LT recipients and seropositivity of CMV, HSV-1 and 2, EB viral capsid antigen (EBVCA) and VZV in LT recipients and their reactivation. METHODS: Pre-transplant data for IgG and IgM for CMV (and donor), HSV-1 and -2, EB viral capsid antigen (VCA) and VZV were available for 153 recipients. All recipients were on ganciclovir or valganciclovir prophylaxis for three months after LT. For reactivation rates, findings of post-transplant CMV quantitative reverse transcription polymerase chain reaction (CMV qRT-PCR) assay were associated with pre-transplant serological profile. RESULTS: Of the 153 LT recipients, 131 were men (85.6%). The median age of LT was 46 yr (range 9 months-71 yr). Overall exposure to CMV was 71.8 per cent followed by EB VCA (61.4%) and VZV (49.6%). Susceptibility to both HSV-1 and -2 was high across all decades (P<0.001). Seropositivity of CMV in donor was 90.9 per cent (100 out of 110). Post-transplant CMV qRT- PCR was positive in 17 (26.6%; 3 in recipient negative) of 64 samples tested. qRT-PCR assay was positive in one out of four (25%) tested for HSV-1 and nine out of 19 (47.4%) tested for EBV. Two recipients tested for HSV-2 and one for VZV were negative. There were three deaths in recipients (D+ R+) who were also positive for CMV qRT PCR. There was one death due to HSV-1 pneumonia. One patient with EBV reactivation developed post-transplant lymphoproliferative disorder two years after transplant. INTERPRETATION & CONCLUSIONS: Transplant recipient were at highest risk of acquiring HSV-1 and -2 more so for HSV-2. CMV exposure in transplant recipients and donors were very high and at greatest risk for recipient reactivation rate. Despite this, death related to CMV reactivation was low.

HRQOL using SF36 (generic specific) in liver cirrhosis.

Health-related quality of life (HRQOL) is influenced by the disease state, associated complications and their management. In patients with liver cirrhosis co-morbidity, severity of liver disease and their complications are likely to affect the QOL. The aim of the study was to determine the factors that are likely to influence the domains of HRQOL using SF-36 in patients with liver cirrhosis. For the study, 149 patients with liver cirrhosis were compared with age-gender matched healthy controls for physical and mental components of SF-36 score and the effects of age, co-morbidity severity of liver disease and complications of liver cirrhosis on HRQOL were assessed using the same questionnaire. Results of the study showed that except for body pain, all the patients had a significantly low individual and composite domain score (p-value <0.0001) compared to age-gender matched controls. Patients below 45 years, Child-Turcotte-Pugh (CTP) C, a high model for end-stage liver disease (MELD) and higher rates of complication had low scores for body pain (KW p <0.005) and those above 55 years, for physical function (p <0.05). Both the physical components had a major impact on mental composite score (MCS) (KW p <0.05). Co-morbidity that included diabetes, hypertension and hypothyroid states in various combinations had no effect on SF-36 scores while co-morbid conditions like musculoskeletal pain, arthralgia etc. affected physical domains (physical function, body pain and role physical) and physical component score (PCS) (KW p <0.01 to <0.0001). By linear regression, MELD had a direct and significant association with overall PCS and mental component score (MCS).

Correction: Occurrence of Diverse Antimicrobial Resistance Determinants in Genetically Unrelated Biocide Tolerant Klebsiella pneumoniae.

[This corrects the article DOI: 10.1371/journal.pone.0166730.].

Combination of TACE and Sorafenib Improves Outcomes in BCLC Stages B/C of Hepatocellular Carcinoma: A Single Centre Experience

ABSTRACT Background & Aim. Transarterial chemoembolization (TACE) or sorafenib is recommended for hepatocellular carcinoma BCLC stages B and C respectively. We studied the role of combination of TACE and sorafenib in BCLC stages B/C. Material and methods. We undertook an observational study on a cohort of cirrhotics with HCC from August 2010 through October 2014. Patients in BCLC stages B/C who had received TACE and/or sorafenib were included. mRECIST criteria were used to assess tumor response. The primary end point was overall survival. Results. Out of 124 patients, 47.6% were in BCLC-B and 52.4% in BCLCC. Baseline characteristics were comparable. The predominant etiology was cryptogenic (37.2% and 38.5%, p = NS). 49.1% in BCLC-B and 56.9% in BCLC-C had received TACE+sorafenib. In BCLC-B, the overall survival improved from 9 months (95% CI 6.3-11.7) using TACE only to 16 months (95% CI 12.9-19.1) using TACE+sorafenib (p < 0.05). In BCLC-C, addition of TACE to sorafenib improved the overall survival from 4 months (95%CI 3-5) to 9 months (95%CI 6.8-11.2) (p < 0.0001). As per mRECIST criteria, patients on TACE+sorafenib had reduced progressive disease (37.8% vs. 83.3%), improved partial response (43.2% vs. 3.3%) and one had complete response compared to those on sorafenib alone (p < 0.0001) in BCLC-C but not in BCLC-B group. Hand foot syndrome was noted in 27.7% patients on sorafenib and post TACE syndrome in 80.2% patients, but both were reversible. No major adverse events were noted. Conclusion. TACE+sorafenib was more effective than TACE or sorafenib alone in HCC BCLC stages B or C with a significant survival benefit and improved tumour regression especially in BCLC-C patients.

Combination of TACE and Sorafenib Improves Outcomes in BCLC Stages B/C of Hepatocellular Carcinoma: A Single Centre Experience.

BACKGROUND AND AIM: Transarterial chemoembolization (TACE) or sorafenib is recommended for hepatocellular carcinoma BCLC stages B and C respectively. We studied the role of combination of TACE and sorafenib in BCLC stages B/C. MATERIAL AND METHODS: We undertook an observational study on a cohort of cirrhotics with HCC from August 2010 through October 2014. Patients in BCLC stages B/C who had received TACE and/or sorafenib were included. mRECIST criteria were used to assess tumor response. The primary end point was overall survival. RESULTS: Out of 124 patients, 47.6% were in BCLC-B and 52.4% in BCLCC. Baseline characteristics were comparable. The predominant etiology was cryptogenic (37.2% and 38.5%, p = NS). 49.1% in BCLC-B and 56.9% in BCLC-C had received TACE+sorafenib. In BCLC-B, the overall survival improved from 9 months (95% CI 6.3-11.7) using TACE only to 16 months (95% CI 12.9-19.1) using TACE+sorafenib (p < 0.05). In BCLC-C, addition of TACE to sorafenib improved the overall survival from 4 months (95%CI 3-5) to 9 months (95%CI 6.8-11.2) (p < 0.0001). As per mRECIST criteria, patients on TACE+sorafenib had reduced progressive disease (37.8% vs. 83.3%), improved partial response (43.2% vs. 3.3%) and one had complete response compared to those on sorafenib alone (p < 0.0001) in BCLC-C but not in BCLC-B group. Hand foot syndrome was noted in 27.7% patients on sorafenib and post TACE syndrome in 80.2% patients, but both were reversible. No major adverse events were noted. CONCLUSION: TACE+sorafenib was more effective than TACE or sorafenib alone in HCC BCLC stages B or C with a significant survival benefit and improved tumour regression especially in BCLC-C patients.

Occurrence of Diverse Antimicrobial Resistance Determinants in Genetically Unrelated Biocide Tolerant Klebsiella pneumoniae.

Nosocomial infections due to Klebsiella pneumoniae is a significant problem in health care settings worldwide. In this study, we examined the antimicrobial susceptibility, genetic profiles and mechanisms of antibiotic resistance in K. pneumoniae isolates of Indian origin. To our knowledge this is the first report demonstrating the high prevalence of ß-lactamases, aminoglycoside modifying enzymes, quinolone resistance genes besides demonstrating the involvement of active efflux in K. pneumoniae Indian isolates. This study has enabled us to correlate the phenotypic and genotypic characteristics in K. pneumoniae, providing an important base for continued monitoring and epidemiological studies of this emerging nosocomial pathogen in Indian hospitals.

Composition of gallbladder bile in healthy individuals and patients with gallstone disease from north and South India.

BACKGROUND: Gallstones (GS) in south India (SI) are predominantly pure pigment or mixed, while in North India (NI), these are either pure cholesterol or mixed. While cholesterol rich gallbladder (GB) bile predicts cholesterol GS, constituent of bile in primary pigment GS is not known. We compared the composition of GB bile from healthy liver donors and patients with GS from north and south India. METHODS: Gallbladder bile from healthy liver donors from north (10) and south India (8) served as controls. Cases were patients from north (21) and south India (17) who underwent cholecystectomy for GS disease. Gallbladder bile from both cases and controls was analyzed for cholesterol, lecithin (phospholipid), and bile salts. Gallstones were classified as cholesterol, mixed, and pigment based on morphology and biochemical analysis. RESULTS: The median cholesterol concentration in control bile from north was significantly high compared to south (p<0.001) with no difference in lecithin and bile salts (p NS). Except for one sample each from north and south, the cholesterol solubility of controls was within the critical micellar zone. Mixed GS were most frequent in north India (61.9 %) while pigment GS dominated in south (61.9 %). The median cholesterol concentration in bile samples of cholecystectomy patients from north India was significantly high GS (p < 0.00001) with significant lowering of bile salts and lecithin (p < 0.00001). In south India, patients with mixed GS had high cholesterol content in bile compared to controls and patients with pigment GS; bile in latter had significantly higher concentration of bile salt compared to controls and mixed GS. The ternary plot confirmed the composition of GB bile from north and south India. CONCLUSIONS: Gallbladder bile in controls and patients with GS from north India had significantly high cholesterol concentration. In south India, patients with mixed GS had cholesterol rich bile while pigment GS had higher concentrations of bile salts.

Donor Outcomes in Living Donor Liver Transplantation-Analysis of 275 Donors From a Single Centre in India.

BACKGROUND: Live donor liver transplantation is the predominant form of liver transplantation in India and in most Asian countries. Donor outcome reports are an important source of information to be shared with prospective donors at the time of informed consent. This is the first donor outcome series from India. METHODS: Analysis of donor characteristics and morbidity of 275 live donors from a single large volume center is documented. RESULTS: Two hundred seventy-five patients donated from November 2009 to October 2014, 144 were women and 131 were men, 180 donated to adults and 95 donated to children. Right lobe donors were majority at 62.2% followed by left lateral segment 28%. Two thirds of the live donors did not have any morbidity; 114 complications were encountered in 85 patients. The complications were graded as per Clavien 5 tier grading and major morbidity (grade III b, grade IV grade V) was 4.36%. Postoperative biliary complication was seen in 3 donors. CONCLUSIONS: This large single-center study is the first donor outcome report from India, and the results are comparable to other published donor series. Documentation and regular audit of donor outcomes is important to help improve the safety of donor hepatectomy and to provide a database for informed consent of prospective donors.

Functional Characterization of AbeD, an RND-Type Membrane Transporter in Antimicrobial Resistance in Acinetobacter baumannii.

BACKGROUND: Acinetobacter baumannii is becoming an increasing menace in health care settings especially in the intensive care units due to its ability to withstand adverse environmental conditions and exhibit innate resistance to different classes of antibiotics. Here we describe the biological contributions of abeD, a novel membrane transporter in bacterial stress response and antimicrobial resistance in A. baumannii. RESULTS: The abeD mutant displayed ~ 3.37 fold decreased survival and >5-fold reduced growth in hostile osmotic (0.25 M; NaCl) and oxidative (2.631 µM-6.574 µM; H2O2) stress conditions respectively. The abeD inactivated cells displayed increased susceptibility to ceftriaxone, gentamicin, rifampicin and tobramycin (~ 4.0 fold). The mutant displayed increased sensitivity to the hospital-based disinfectant benzalkonium chloride (~3.18-fold). In Caenorhabditis elegans model, the abeD mutant exhibited (P<0.01) lower virulence capability. Binding of SoxR on the regulatory fragments of abeD provide strong evidence for the involvement of SoxR system in regulating the expression of abeD in A. baumannii. CONCLUSION: This study demonstrates the contributions of membrane transporter AbeD in bacterial physiology, stress response and antimicrobial resistance in A. baumannii for the first time.

A study of gender-wise risk association between fatty liver and metabolic syndrome components (Asia-Pacific criteria) in a South Indian urban cohort.

BACKGROUND: Metabolic syndrome (MS) is associated with fatty liver (FL) disease. Gender differences in this association are not known. AIM: The aim of the present study was to determine gender-wise association between FL and MS components (using Asia-Pacific guidelines 2007) in an urban south Indian cohort with normal liver function tests (LFT). METHODS: Records of consecutive attendees of a Master Health Check up program were reviewed for age, gender, body mass index (BMI), blood pressure, fasting blood sugar (FBS), high-density lipoproteins, triglyceride (TG) levels, presence of FL by ultrasound. The cohort was grouped gender-wise as FL and nonfatty liver (NFL). Foreign nationals; those with alcohol intake >20 g/day; and those with diabetes, hypertension, hypertriglyceridemia, chronic liver disease, or abnormal LFT were excluded. STATISTICS: Chi-square, gender-wise univariate and logistic regression analyses of each MS component for FL, relative risk (RR), and 95 % confidence interval (CI) for significant factors (p < 0.05 and RR or log odds >1.5) were calculated. RESULTS: Of the 1,075 (63 % males) cases included, 45.8 % had FL. Gender (log odds 1.6 compared to women) and BMI ≥25 kg/m(2) (RR 1.6 % to 95 % CI 1.3 to 1.9; log odds 2.2) were the only factors associated with FL in men. In women, age ≥40 years (log odds 2.3), fasting blood sugar (FBS) ≥100 mg/dL (RR 1.8-1.4 to 2.3; log odds 1.9), and TG ≥150 mg/dL (RR 1.7-1.3 to 2.1; log odds 1.7) were independently associated with FL. CONCLUSION: There was a gender-wise difference in MS components associated with hepatic steatosis and normal LFT in a south Indian urban cohort.