Association of Putative Virulence Genes with HEp-2 Cell Adherence and Biofilm Production in Enteroaggregative E. coli Strains Isolated from Acute Diarrheal and Healthy Children, India

Enteroaggregative Escherichia coli (EAEC) is an emerging enteric pathogen that causes acute and chronic diarrhea in developed and industrialized countries in children. EAEC colonizes the human intestine and this ability to form colonies and biofilm is an important step in pathogenesis. Here, we investigated the relationship between known or putative 22 EAEC virulence genes and biofilm formation in isolates derived from acute diarrhea and healthy children and their aggregative adherence (AA) pattern with Hep-2 cell lines. A total of 138 EAEC isolates were recovered from 1210 stool samples from children (age < 10 years) suffering from acute diarrhea and 33 EAEC strains isolated from 550 healthy children (control group) of different Anganwadi centers in Chandigarh region were included. Polymerase chain reaction using the primer pair pCVD432 identified E. coli isolates as EAEC. A total of 22 virulence-related genes have been identified using M-PCR chain reactions. The crystal violet method was used for the quantitative biofilm assay. Aggregative adherence assay was also studied using HEp-2 cell lines. Of 138 EAEC isolates from the acute diarrheal group, 121 (87.6%) EAEC isolates produced biofilm. In our findings, typical EAEC (62%) isolates were strong biofilm producers (37.5%) in the diarrheal group. Among adhesive variants, agg4A (39.6%) and aggA (21.6%) were the most common and were statistically significant (p = 0.01 and p = 0.03 respectively). We reported that the aggR gene along with the typical AA pattern was present in 71.4% of the EAEC strains in the diarrheal group, whereas it was present in 44% of the control group. Other aggR non-dependent genes like ORF3 and eilA may also lead to biofilm formation. In conclusion, there is significant heterogeneity in putative virulence genes of EAEC isolates from children and biofilm formation is associated with the combination of many genes.

Extensively Drug-Resistant Klebsiella pneumoniae Associated with Complicated Urinary Tract Infection in Northern India

Klebsiella pneumoniae (Kp), which is associated with hospital-acquired infections, is extensively drug-resistant (XDR), making treatment difficult. Understanding the genetic epidemiology of XDR-Kp can help determine its potential to be hypervirulent (hv) through the presence of siderophores. We characterized the genomes of 18 colistin-resistant XDR-Kp isolated from 14 patients with complicated tract infection at an Indian healthcare facility. The 18 organisms comprised the following sequence types (STs): ST14 (n = 9), ST147 (n = 5), ST231 (n = 2), ST2096 (n = 1), and ST25 (n = 1). Many patients in each ward were infected with the same ST, suggesting a common source of infection. Some patients had recurrent infections with multiple STs circulating in the ward, providing evidence of hospital transmission. β-lactamase genes (blaCTX-M-1, blaSHV, and blaampH) were present in all isolates. blaNDM-1 was present in 15 isolates, blaOXA-1 in 16 isolates, blaTEM-1D in 13 isolates, and blaOXA-48 in 3 isolates. Disruption of mgrB by various insertion sequences was responsible for colistin resistance in 6 isolates. The most common K-type among isolates was K2 (n = 10). One XDR convergent hvKp ST2096 mutation (iuc+ybt+blaOXA-1+blaOXA-48) was associated with prolonged hospitalization. Convergent XDR-hvKp has outbreak potential, warranting effective antimicrobial stewardship and infection control.

Neisseria mucosa: A not so Benign Culprit of urinary tract infection: A case report

Neisseria mucosa is saprophytic human commensal but reported as a causative agent in a couple of urinary tract infections [UTI] in susceptible individuals. In the present case, a young girl with long standing neurological problems presented with bladder outlet obstruction and fever. Her urine culture yielded Neisseria mucosa which was susceptible to broad spectrum penicillins, aminoglycosides, cephalosporins, ciprofloxacin, and azithromycin. She recovered with suitable dosage of amoxicillin clavulanic acid and was discharged. Isolation of N. mucosa here becomes clinically significant as this girl had various ureteric and lower limb weaknesses in past and was symptomatic for UTI with this infection.

Diptheroids can cause nosocomial UTI and be multidrug resistant: A case report of Corynebacterium striatum, first from India

Gram positive bacilli in the urine are usually dismissed as contaminants in urine specimens as these are commensal flora of skin and mucous membranes. Corynebacterium species were misidentified in the past due to complex biochemicals but the advent of modern diagnostics has made their identification quicker and accurate. Corynebacterium species have recently emerged as pathogens of nosocomial outbreak potential. C. striatum has been identified as opportunistic nosocomial pathogen causing various infections. We report first case of C. striatum as nosocomial urinary tract infection (UTI) pathogen in a child with bilateral renal disease. C. striatum causing UTI is very rarely reported.

Differential invasiveness & expression of antimicrobial peptides in Shigella serotypes

Background & objectives

The study of Shigella pathogenesis at present is severely hampered by the lack of a relevant animal model that replicates human bacillary dysentery. Different Shigella serogroups cause varying severity of clinical illness. Ex vivo colonization of Shigella flexneri, S. dysenteriae and S. sonnei were characterized in human paediatric colonic pinch biopsies in the in vitro organ culture (IVOC) model to study the invasiveness of Shigella by gentamicin protection assay (GPA). Furthermore, the expression of antimicrobial peptides (AMPs) in response to different serotypes of Shigella was also studied in IVOC model.

Methods

IVOC explants were inoculated with 109 colony forming units of different serotypes of Shigella and recovery of bacteria studied. Histopathological analysis was carried out to study inflammatory immune responses. GPA was done to elucidate the invasiveness of different serotypes of Shigella. Secretions of AMPs were measured by enzyme-linked immunosorbent assay (ELISA). Western blotting was performed to check the expression of AMPs and nuclear factor kappa B in IVOC explants.

Results

After 24 h post-infection, the colon biopsies showed intense inflammatory reaction. In both IVOC and GPA, S. dysenteriae 1 was the most invasive as compared to S. flexneri and S. sonnei. S. sonnei was the least invasive. ELISA demonstrated that S. sonnei dampened the HBD (human β-defensin)-2 responses whereas there was augmentation by S. dysenteriae and there was a modest but non-significant increase by S. flexneri. A modest increase in HBD-3 by S. sonnei and S. flexneri was observed but was not found to be significant. However, western blotting data showed upregulation of all AMPs by all serotypes. Western blotting is more sensitive than ELISA.

Interpretation & conclusions

In the present study, differences in invasiveness and AMP production induced by different serotypes of Shigella were found. Human intestinal IVOC represents a model system to investigate early interaction between pathogenic bacteria and the human gut.

Computational Guided Drug Targets Identification against Extended-Spectrum Beta-Lactamase-Producing Multi-Drug Resistant Uropathogenic Escherichia coli

Urinary tract infections (UTIs) are one of the most frequent bacterial infections in the world, both in the hospital and community settings. Uropathogenic Escherichia coli (UPEC) are the predominant etiological agents causing UTIs. Extended-spectrum beta-lactamase (ESBL) production is a prominent mechanism of resistance that hinders the antimicrobial treatment of UTIs caused by UPEC and poses a substantial danger to the arsenal of antibiotics now in use. As bacteria have several methods to counteract the effects of antibiotics, identifying new potential drug targets may help in the design of new antimicrobial agents, and in the control of the rising trend of antimicrobial resistance (AMR). The public availability of the entire genome sequences of humans and many disease-causing organisms has accelerated the hunt for viable therapeutic targets. Using a unique, hierarchical, in silico technique using computational tools, we discovered and described potential therapeutic drug targets against the ESBL-producing UPEC strain NA114. Three different sets of proteins (chokepoint, virulence, and resistance genes) were explored in phase 1. In phase 2, proteins shortlisted from phase 1 were analyzed for their essentiality, non-homology to the human genome, and gut flora. In phase 3, the further shortlisted putative drug targets were qualitatively characterized, including their subcellular location, broad-spectrum potential, and druggability evaluations. We found seven distinct targets for the pathogen that showed no similarity to the human proteome. Thus, possibilities for cross-reactivity between a target-specific antibacterial and human proteins were minimized. The subcellular locations of two targets, ECNA114_0085 and ECNA114_1060, were predicted as cytoplasmic and periplasmic, respectively. These proteins play an important role in bacterial peptidoglycan biosynthesis and inositol phosphate metabolism, and can be used in the design of drugs against these bacteria. Inhibition of these proteins will be helpful to combat infections caused by MDR UPEC.

Are non-lactose-fermenting Escherichia coli important diarrhoeal pathogens in children and adults?

Introduction

Diarrhoeagenic Escherichia coli (DEC) remains one of the major causes of acute diarrhoea episodes in developing countries. The percentage of acute diarrhoea cases caused by DEC is 30-40 % in these countries. Approximately 10% of E. coli isolates obtained from stool specimens have been reported to be non-lactose-fermenting (NLF). The available literature is sparse regarding the pathogenicity of NLF E. coli causing infectious diarrhoea.

Aim

We aimed to elucidate the importance of NLF E. coli in causing diarrhoea in both adults and children by detecting various DEC pathotypes among NLF E. coli in stool samples taken from gastroenteritis cases.

Material and Methods

A total of 376 NLF E. coli isolates from 3110 stool samples from diarrhoea/gastroenteritis patients were included in the study. Up to three NLF colonies that were not confirmed as Vibrio cholerae , Aeromonas spp., Salmonella spp. or Shigella spp., but were identified as E. coli using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), were carefully picked up from each MacConkey agar plate and then meticulously streaked onto freshly prepared, sterilized nutrient agar plates, and biochemical reactions were conducted. Multiplex PCR was conducted for the EAEC, EPEC, ETEC and EHEC pathotypes and PCR for the ipaH gene was conducted for EIEC. The disc diffusion method was used for antibiotic sensitivity testing.

Results

Using multiplex PCR and ipaH PCR, a total of 63 pathotypes of DEC were obtained, with EAEC being the most predominant (n=31) followed by EIEC (n=22), EPEC (n=8) and ETEC (n=2). To further differentiate EIEC from Shigella , additional biochemical tests were performed, including acetate utilization, mucate and salicin fermentation, and aesculin hydrolysis. Antimicrobial susceptibility testing (AST) showed that maximum resistance was seen against ciprofloxacin (82.5 %) followed by ampicillin (77.8 %) and cotrimoxazole (68.2 %), and minimum resistance was seen against ertapenem (4.8 %).

Conclusion

In our study two pathotypes (EAEC, EIEC) were predominant among NLF E. coli and these were not only important aetiological agents in children, but also in adults. Our study also sheds light on the epidemiology of EIEC, which is one of the most neglected DEC pathotypes, as hardly any microbiological laboratories process NLF E. coli for EIEC.

Vibrio Phage VMJ710 Can Prevent and Treat Disease Caused by Pathogenic MDR V. cholerae O1 in an Infant Mouse Model

Cholera, a disease of antiquity, is still festering in developing countries that lack safe drinking water and sewage disposal. Vibrio cholerae, the causative agent of cholera, has developed multi-drug resistance to many antimicrobial agents. In aquatic habitats, phages are known to influence the occurrence and dispersion of pathogenic V. cholerae. We isolated Vibrio phage VMJ710 from a community sewage water sample of Manimajra, Chandigarh, in 2015 during an outbreak of cholera. It lysed 46% of multidrug-resistant V. cholerae O1 strains. It had significantly reduced the bacterial density within the first 4-6 h of treatment at the three multiplicity of infection (MOI 0.01, 0.1, and 1.0) values used. No bacterial resistance was observed against phage VMJ710 for 20 h in the time-kill assay. It is nearest to an ICP1 phage, i.e., Vibrio phage ICP1_2012 (MH310936.1), belonging to the class Caudoviricetes. ICP1 phages have been the dominant bacteriophages found in cholera patients' stools since 2001. Comparative genome analysis of phage VMJ710 and related phages indicated a high level of genetic conservation. The phage was stable over a wide range of temperatures and pH, which will be an advantage for applications in different environmental settings. The phage VMJ710 showed a reduction in biofilm mass growth, bacterial dispersal, and a clear disruption of bacterial biofilm structure. We further tested the phage VMJ710 for its potential therapeutic and prophylactic properties using infant BALB/c mice. Bacterial counts were reduced significantly when phages were administered before and after the challenge of orogastric inoculation with V. cholerae serotype O1. A comprehensive whole genome study revealed no indication of lysogenic genes, genes associated with possible virulence factors, or antibiotic resistance. Based on all these properties, phage VMJ710 can be a suitable candidate for oral phage administration and could be a viable method of combatting cholera infection caused by MDR V. cholerae pathogenic strains.

Evaluation of an automated rapid urine culture method for urinary tract infection: Comparison with gold standard conventional culture method

PURPOSE

Urinary tract infection is one of the most prevalent disease affecting people from all age groups. For its diagnosis, conventional culture and antibiotic susceptibility is the gold standard. However, its major limitation is that the results take minimum of 24 ​h and antibiotic susceptibility is available after 48 ​h. Automated culture methods having comparable sensitivity and specificity as compared to conventional culture should be evaluated for routine diagnostics. With this aim we evaluated the diagnostic accuracy of automated urine culture method HB&L uroquattro by comparing with the gold standard conventional culture method.

MATERIALS AND METHODS

A total of 1220 urine samples were included in the study. Semi-quantitative urine culture was performed using standard methods on cysteine lactose electrolyte deficient medium. For the automated culture, HB&L Uroquattro (Alifax, Polverara, PD, Italy), standard guidelines given in the manual of the instrument were followed. Diagnostic performance in terms of sensitivity, specificity, positive and negative likelihood ratios, positive and negative predictive values were calculated.

RESULTS

Based on the final interpretation of conventional culture for the total 1220 samples, 26 samples (2.1%) showed major non-concordance as they were identified as sterile by HB&L but had significant growth by conventional culture and 19.9% showed minor non-concordance. At 100-999 colony forming unit/ml, HB&L has high negative predictive value i.e. 96.6% with 95% CI (95.2%-97.6%) and sensitivity i.e. 92.66% with 95% CI of (89.42%-95.15%).

CONCLUSION

The HB&L Uroquattro seems to be a reliable instrument to obtain urine microbiological results in a timely manner. This technique can give presumptive report to the clinician within 5 ​h only for initiation of empirical antibiotics in cases of positive results.

Effect on growth performance, carcass traits, and myostatin gene expression in Aseel chicken fed varied levels of dietary protein in isocaloric energy diets

A study was conducted to assess the effect of feeding different crude protein (CP) levels with isocaloric metabolizable energy (ME) diets on growth performance, carcass traits, and myostatin (MSTN) gene expression of Aseel chicken during 0 to 16 weeks of age. A total of two hundred and ten day-old Aseel chickens were randomly allotted to seven dietary treatment groups. Each group had thirty chicks distributed into three replicates of ten chicks in each. Experimental diets were formulated to have varying levels of CP, viz. 18.5, 19.0, 19.5, 20.0, 20.5, 21.0, and 21.5%, with isocaloric energy of 2800 kcal ME/kg diets of mash feed fed to birds in a completely randomized design. Different CP levels had a significant effect (P < 0.05) on the body weight gain (BWG) of Aseel chicken. At the end of 16 weeks of age, the group fed 21% CP gained 223.53 g more than the lowest CP (18.5%)-fed group. The different CP levels did not significantly (P > 0.05) influenced the feed intake of all treatment groups, but numerically highest feed intake was observed in the lowest CP (18.5%)-fed group. However, significant differences in feed efficiency (FE) appeared from the 13th week only with the 21.0% CP-fed group showing the best FE until the 16th week (3.86 to 4.06). The maximum dressing % (70.61) was observed by the 21% CP-fed group. The CP 21% diet down-regulated the MSTN gene expression in breast muscle tissue to 0.07 folds when compared to the diet of CP 20%. The best economical coordinates for maximum performance for Aseel chicken appeared to be CP of 21% and ME of 2800 kcal/kg to achieve the best FE of 3.86 at the earliest age of 13 weeks. In conclusion, 21% CP in an isocaloric diet of 2800 kcal ME/kg, in Aseel chickens, would be optimum to improve the growth performance at maximum in terms of BWG and FE up to 16 weeks of age.

Identification and functional annotation of hypothetical proteins of uropathogenic Escherichia coli strain CFT073 towards designing antimicrobial drug targets

Urinary tract infections are a serious health concern worldwide, especially in developing countries. Escherichia coli strain CFT073 is a highly virulent pathogenic bacterial strain. CFT073 proteome contains 4897 proteins, out of which 992 have been classified as hypothetical proteins. Identification and characterization of hypothetical proteins can aid in the selection of targets for drug design. In this study, we studied the hypothetical proteins from the UPEC strain CFT073 using various computational tools. By NCBI-CDD, 376 protein sequences showed conserved domains. Based on the functional motifs in their primary sequences, we classified these 376 hypothetical proteins into 7 functional categories. Further KEGG database was used to find the roles of these hypothetical proteins in several pathways. Protein interaction network analysis of hypothetical proteins identified 53 proteins as highly interacting metabolic proteins. Virulence factor analysis of the proteins identified 8 proteins as virulent. We conducted a non-homology search for the identified proteins of UPEC in the available human proteome. We observed that 35 proteins are non-homologous to humans and hence could be selected for drug designing targets. Qualitative characterization of the selected 35 non-homologous hypothetical proteins including essentiality analysis and evaluation of druggability by similarity search against drug bank database was performed. Out of these 35 proteins, three-dimensional structures of six proteins (NP_752562.1, NP_756345.1, NP_754893.1, NP_756600.2, NP_755264.1 and NP_752994.1) could be successfully modelled. These new annotations can help to better understand disease mechanisms at the molecular level, as well as provide new targets for drug development against the UPEC strain CFT073.Communicated by Ramaswamy H. Sarma.

Whole genome sequencing and in vitro activity data of Escherichia phage NTEC3 against multidrug-resistant Uropathogenic and extensively drug-resistant Uropathogenic E. coli isolates

This data article describes the whole-genome sequencing and in vitro activity data of Escherichia phage NTEC3 isolated from a community sewage sample in Chandigarh, India. The phage NTEC3 was active against multi-drug-resistant (MDR) and extensively drug-resistant (XDR) biofilm-forming Uropathogenic Escherichia coli (UPEC) strains. The genome of this phage was linear, double-stranded, and 44.2 kb long in size. A total of 72 ORFs (open reading frames) were predicted and 30 ORFs were encoded for functional proteins. The phage belonged to the Kagunavirus genus of the Siphoviridae family. Phylogenetic analysis using DNA polymerase was performed to understand the phage evolutionary relationships. Genes encoding for lysogeny, virulence, toxins, antibiotic resistance, and the CRISPR/CRISPR-like system were not found during screening. The annotated genome was deposited in Genbank under the accession number OK539620.

Repurposing of FDA approved drugs against uropathogenic Escherichia coli: In silico, in vitro, and in vivo analysis

Urinary tract infections (UTIs) are a serious health concern worldwide. Treatment of UTIs is becoming a challenge as uropathogenic Escherichia coli (UPEC), which is the most common etiological agent, has developed resistance to the main classes of antibiotics. Small molecules that interfere with metabolic processes rather than growth are attractive alternatives to conventional antibiotics. Repurposing of already known drugs for treating infectious diseases could be an attractive avenue for finding novel therapeutics against infections caused by UPEC. Virtual screenings enable the rapid and economical identification of target ligands from large libraries of compounds, reducing the cost and time of traditional drug discovery. Moreover, the drugs that have been approved by the FDA have low cytotoxicity and good pharmacological characteristics. In this work, we targeted the HisC enzyme of the histidine biosynthetic pathway as enzymes of this pathway are absent in humans. We screened the library of FDA-approved drugs against HisC via molecular docking, and four hits (Docetaxel, Suramin, Digitoxin, and Nystatin) showing the highest binding energy were selected. These were further tested for antibacterial activity, which was observed only for Docetaxel (MIC value of 640 μg/ml); therefore, Docetaxel was further tested for its efficacy in vivo in murine catheter UTI model and antibiofilm activity using crystal violet staining and scanning electron microscopy. Docetaxel inhibited biofilm formation and reduced the bacterial load in urine, kidney, and bladder. Docking studies revealed that Docetaxel acts by blocking the binding site of HisC to the native substrate by competitive inhibition. Docetaxel may be a potential new inhibitor for UPEC with antibacterial and antibiofilm capability.

Characterization, genome analysis and in vitro activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant and extensively drug-resistant biofilm-forming uropathogenic Escherichia coli isolates, India

AIM

We aimed to study host range, stability, genome and antibiofilm activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant (MDR) and extensively drug-resistant (XDR) biofilm-forming uropathogenic Escherichia coli isolates.

METHODS AND RESULTS

A novel lytic phage vB_EcoA_RDN8.1 active against UPEC strains resistant to third-generation cephalosporins, fluoroquinolones, aminoglycosides, imipenem, beta-lactamase inhibitor combination and polymyxins was isolated from community raw sewage water of Chandigarh. It exhibited a clear plaque morphology and a burst size of 250. In the time-kill assay, the maximum amount of killing was achieved at MOI 1.0. vB_EcoA_RDN8.1 belongs to the family Autographiviridae, has a genome size of 39.5 kb with a GC content of 51.6%. It was stable over a wide range of temperatures and pH. It was able to inhibit biofilm formation which may be related to an endolysin encoded by ORF 19.

CONCLUSIONS

The vB_EcoA_RDN8.1 is a novel lytic phage that has the potential for inclusion into phage cocktails being developed for the treatment of urinary tract infections (UTIs) caused by highly drug-resistant UPEC.

SIGNIFICANCE AND IMPACT OF THE STUDY

We provide a detailed characterization of a novel lytic Escherichia phage with antibiofilm activity having a potential application against MDR and XDR UPEC causing UTIs.

Antimicrobial resistant Shigella in North India since the turn of the 21st century

PURPOSE

The ubiquitous presence and rampant spread of antibiotic resistant strains of Shigella spp is a major public health concern. Therefore, monitoring the trends of antimicrobial resistance in them is essential.

METHODS

A total of 15440 stool samples were inoculated on MacConkey agar, lysine deoxycholate agar and Selenite F enrichment broth from 2001 to 2015.Out of 491 shigellae isolated, 250 isolates were recovered from our culture collection. Antimicrobial susceptibility was performed by Kirby Bauer disc diffusion method, E-test and phenotypic resistance screening for ESBL and AmpC production was performed. For the detection of beta-lactamase genes, PCR for blaTEM, blaSHV, blaOXA, blaCTX-M-15, CMY-2 and mphA PCR in isolates with decreased susceptibility to azithromycin(DSA) was performed.

RESULTS

S. flexneri (n ​= ​173) was most common, followed by S.dysenteriae (n ​= ​24), S.sonnei (n ​= ​23), S.boydii (n ​= ​10) and Non agglutinating Shigella (NAG, n ​= ​20). A see-saw pattern in the prevalence of S. flexneri and S. dysenteriae and rising prevalence of S. sonnei and NAG was seen. Majority (77%) of the isolates had MICs >4 ​mg/L for ciprofloxacin and >50% had high MIC₉₀ (12 ​mg/L) for ceftriaxone and cefepime (8 ​mg/L). Nearly 20% of S.flexneri were resistant to third generation cephalosporin by disc diffusion and 33.7% had MIC ≥1 ​μg/mL. Among the ceftriaxone resistant isolates (n ​= ​29) the blaTEM beta-lactamase resistance gene was seen in all, blaCTX-M-15 in 37%, blaCMY-2 in 45.6% and blaOXA in 52%. The first report of DSA at our institute was in 2001 (n ​= ​1, 2.5%) which increased to 35.1% (n ​= ​40) in 2011-15. The isolates with DSA included S. flexneri (n ​= ​40), S. boydii (n ​= ​4) and S. sonnei (n ​= ​1) and plasmid mediated resistance to azithromycin by mphA gene was detected in 19 out of 40 isolates of S. flexneri.

CONCLUSION

Global emergence of resistance Shigella is a matter of concern and calls for systematic monitoring and periodic updates of countrywide and local antibiogram.

Phenotypic and genotypic characterization of antimicrobial resistance in clinical isolates of Vibrio cholerae over a decade (2002-2016)

PURPOSE

Emergence and spread of resistance among Vibrio cholerae have become a global public health problem. In India, no consolidated data is available on antimicrobial susceptibility patterns and antibiotic resistance genes.

METHODS

A total of 110 representative isolates obtained over a period of 14 years were included. Antimicrobial susceptibility was tested by disc diffusion and micro broth dilution. Presence of 13 antimicrobial resistance genes was ascertained by using PCR.

RESULTS

Antimicrobial resistance fluctuated for most of the antibiotics. Resistance to cotrimoxazole in our study was 92.72% and the SXT element was present in all isolates. Resistance to nalidixic acid, tetracycline, and cefotaxime was found to be 98.18%, 7.27%, and 10.9% respectively. Resistance to ampicillin saw a fluctuating trend with a recent fall. Resistance to ciprofloxacin and azithromycin was 12.72% and 29% by MIC. bla_TEM was the most common ESBL gene (94.5%). Other were bla_CMY (26.36%) and bla_NDM (2.7%). We report bla_CTX-M-15 and bla_OXA-48 and ermB for the first time in the world. Newer antimicrobials like prulifloxacin and rifaximin were tested for the first time from India.

CONCLUSIONS

Our study has shown very high levels of resistance to older antibiotics and the emergence of resistance to some of the newer classes of antibiotics. There is an urgent need for increased surveillance studies, rational use of the antimicrobials and preventive measures to control the disease.

Prevalence, Virulence Gene Profiling, and Characterization of Enteroaggregative Escherichia coli from Children with Acute Diarrhea, Asymptomatic Nourished, and Malnourished Children Younger Than 5 Years of Age in India

OBJECTIVE

To study the significance of enteroaggregative Escherichia coli (EAEC) as a pathogen causing acute diarrhea and a commensal in healthy nourished and malnourished children younger than five years of age in the Chandigarh region and to address possible traits of EAEC virulence genes, biofilm formation, phylogroups, and antibiotic resistance that would be correlated with diarrhea or carriage.

STUDY DESIGN

Stool samples were obtained from children with acute diarrhea (n = 548), as well as nourished (n = 550), and malnourished controls without diarrhea (n = 110). E coli isolates were confirmed as EAEC by pCVD432 polymerase chain reaction. Multiplex polymerase chain reactions were used to identify 22 virulence-related genes and phylogeny. Antibiotic susceptibility, adherence, and biofilm-forming potential also were studied.

RESULTS

Overall, 16.6% of children were malnourished. EAEC detection was greater among children with acute diarrhea (16%) than nourished (6%) and malnourished nondiarrheal controls (2.7%). We found an association of EAEC infections with age <2 years (P = .0001) in the diarrheal group. Adhesive variants adhesion fimbriae IV and adhesion fimbriae II were significantly associated with diarrhea. The aggR and aar genes showed a positive and negative association with the severity of disease (P = .0004 and P = .0003). A high degree of multidrug resistance was found (73.8%) in the diarrheal group. Most EAEC strains from the diarrheal group belonged to B2 and D phylogroups, whereas strains from non-diarrheal groups, which belonged to phylogroup B1.

CONCLUSIONS

EAEC is a significant contributor to childhood diarrhea, its presence as a commensal, and the significance of the association of various virulence factors among the EAEC isolated from diarrheal and non-diarrheal stools. These data reinforce the importance of aggR and aar as positive and negative regulators and the contribution of AAF/II and AAF/IV fimbria for the pathobiology of EAEC.

Antimicrobial resistance in Shigella species: Our five years (2015-2019) experience in a tertiary care center in north India

PURPOSE

Shigella is the second leading cause of diarrhoeal mortality especially in children <5 years of age in African and Asian countries. Rapid changes are occurring in the epidemiology of shigellosis and Shigella are increasingly becoming highly drug resistant. To determine the serogroup distribution and antimicrobial resistance of Shigella isolated at our tertiary care centre in North India.

METHODS

A retrospective study was conducted where demographic details along with antimicrobial susceptibility data of Shigella isolated from stool specimens from 1^st January 2015 till 31^st December 2019 were retrieved from records and analyzed by WHONET 2019 software.

RESULTS

Shigella species was isolated in 1.31% (n = 137) of a total of 10,456 stool samples. Males predominated (n = 82; 59.8%) and majority of cases were admitted (n = 94; 68.6%). Children ≤5 years of age (n = 47; 34.3%) were the most commonly affected. Adults in the 21-40 age group contributed 27% of cases (n = 37). Overall, Shigella flexneri (n = 87; 63.5%) was the most common serogroup followed by non-agglutinable Shigella (n = 28; 20.4%) while Shigella sonnei (n = 12, 8.8%) and Shigella boydii (n = 9, 6.6%) fluctuated over the years. Shigella dysenteriae reappeared in 2019 after a hiatus of ten years. Overall, 45.3% (n = 62) of isolates were multidrug resistant to CLSI recommended drugs and high resistance was noted for ampicillin/amoxicillin (68.1%), cotrimoxazole (75.8%) ciprofloxacin (61.5%) and ceftriaxone/cefotaxime (45.2%).

CONCLUSIONS

Shigella have become highly drug resistant to fluoroquinolones and cephalosporins. Community based studies are required to truly assess the burden of AMR in India.

Comparative analysis of virulence determinants, phylogroups, and antibiotic susceptibility patterns of typical versus atypical Enteroaggregative E. coli in India

Enteroaggregative Escherichia coli (EAEC) is an evolving enteric pathogen that causes acute and chronic diarrhea in developed and industrialized nations in children. EAEC epidemiology and the importance of atypical EAEC (aEAEC) isolation in childhood diarrhea are not well documented in the Indian setting. A comparative analysis was undertaken to evaluate virulence, phylogeny, and antibiotic sensitivity among typical tEAEC versus aEAEC. A total of 171 EAEC isolates were extracted from a broad surveillance sample of diarrheal (N = 1210) and healthy children (N = 550) across North India. Polymerase chain reaction (PCR) for the aggR gene (master regulator gene) was conducted to differentiate tEAEC and aEAEC. For 21 virulence genes, we used multiplex PCR to classify possible virulence factors among these strains. Phylogenetic classes were identified by a multiplex PCR for chuA, yjaA, and a cryptic DNA fragment, TspE4C2. Antibiotic susceptibility was conducted by the disc diffusion method as per CLSI guidelines. EAEC was associated with moderate to severe diarrhea in children. The prevalence of EAEC infection (11.4%) was higher than any other DEC group (p = 0.002). tEAEC occurrence in the diarrheal group was higher than in the control group (p = 0.0001). tEAEC strain harbored more virulence genes than aEAEC. astA, aap, and aggR genes were most frequently found in the EAEC from the diarrheal population. Within tEAEC, this gene combination was present in more than 50% of strains. Also, 75.8% of EAEC strains were multidrug-resistant (MDR). Phylogroup D (43.9%) and B1 (39.4%) were most prevalent in the diarrheal and control group, respectively. Genetic analysis revealed EAEC variability; the comparison of tEAEC and aEAEC allowed us to better understand the EAEC virulence repertoire. Further microbiological and epidemiological research is required to examine the pathogenicity of not only typical but also atypical EAEC.

Enteroaggregative E. coli (EAEC) are an increasingly important cause of diarrhea. E. coli belonging to this category cause watery diarrhea, which is often persistent and can be inflammatory. It is also associated with traveler’s diarrhea in children and adults in middle and high-income countries. EAEC are defined by their ability to adhere to epithelial cells in a characteristic stacked brick-like pattern. However, the identification of these pathogenic strains remains elusive because of its heterogeneous nature. Genes that could contribute to the pathogenicity of EAEC encode adhesions, toxins, and other factors. Due to the heterogeneity of EAEC strains and differing host immune responses, not all EAEC infections are symptomatic. A critical factor in both recognizing EAEC pathogenesis and defining typical EAEC (tEAEC) strains is AggR, a transcriptional control for many EAEC virulence genes. The central role of aggR in virulence confers a strong priority to understand its pathogenicity. To identify EAEC, the CVD432 probe has been used. The CVD432 is a DNA probe from pAA plasmid of EAEC, has been reported to be specific for the detection of EAEC. The lack of sensitivity comes from the genetic heterogeneity of the EAEC strains and the wide geographic dispersal of strains. In our study, we performed a large surveillance of EAEC from North India among the pediatric population. Samples were collected by the microbiology staff at the Postgraduate Institute of Medical Education and Research (PGIMER) and referral system labs in Chandigarh (Manimajra), Punjab (Ludhiana), Haryana (Panchkula and Ambala Cantt), Himachal Pradesh (Hamirpur, Shimla, and Tanda), and Uttarakhand (Rishikesh, Rudrapur, and Haridwar)]. PGIMER is the largest tertiary care hospital in North India and serves patients from across Punjab, Jammu and Kashmir, Himachal Pradesh and Haryana. EAEC infections were detected using molecular methods. In our finding, astA, aap, and aggR genes were most frequently found in the EAEC from the diarrheal population. Within tEAEC, this gene combination is present in more than 50% of strains and helps to differentiate tEAEC from aEAEC. Our collection of EAEC strains helps in finding an appropriate marker for the early detection of EAEC. Our signature sequence (astA, aap, and aggR) will be ideal as focus genes for EAEC identification, as well as tEAEC and aEAEC. The multidrug resistance (MDR) was observed in 75.8% of the EAEC strains. tEAEC exhibits resistance to a greater number of antibiotics with respect to aEAEC. The phylogenetic analysis revealed that EAEC phylogeny is diverse and dispersed in all the phylogroups.

Molecular, phylogenetic and antibiotic resistance analysis of enteroaggregative escherichia coli/uropathogenic Escherichia coli hybrid genotypes causing urinary tract infections

Background

Horizontal gene transfer of virulence genes (VGs) from different Escherichia coli pathotypes results in the evolution of hybrid strains. Hybrid genotypes of enteroaggregative E. coli and uropathogenic E. coli (EAEC/UPEC) have been reported in sporadic infections and outbreaks of extraintestinal origin. Yet, their association with routine infections is still underrated.

Materials and Methods

In this study, we analysed 163 isolates of E. coli from cases of urinary tract infection seeking hybrid (EAEC/UPEC) strains. Using multiplex polymerase chain reaction, we investigated VGs (adhesive and toxin genes) of UPEC along with EAEC marker genes (aap and agg R), ast A (toxin genes) and serine protease autotransporters of Enterobacteriaceae, pet (plasmid-encoded toxin) and pic (mucinase gene). Those UPEC strains which had characteristic defining genes of EAEC (agg R/aap or their combination) were considered UPEC/EAEC hybrids.

Results

Molecular predictors of EAEC (aap and aggR) were detected in 20.2% (33/163) of the strains. The pap C was also detected in 36% of the EAEC/UPEC hybrid strains. Phylogenetic analysis revealed that hybrid strains belonged to Group D (60.6%). Nearly 73.8% of UPEC and 75.7% of UPEC/EAEC hybrid strains were multidrug-resistant. Among UPEC isolates, 72.3% and in hybrid UPEC/EAEC, 78.7% isolates were able to produce biofilm.

Conclusions

Our results indicated a closer relationship among EAEC and UPEC, which suggested that some EAEC strains can be potential uropathogens. Ours is a first study documenting the existence of EAEC pathotypes VGs in UPEC strains of nosocomial origin; further studies are required to understand the diarrhoeagenic potential of these hybrids.

Evaluation of matrix assisted laser desorption ionisation-time of flight mass spectrometry in direct identification of bacteriuria from urine samples

Objective

The use of matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI) directly on urine can significantly improve turnaround time for diagnosing urinary tract infection (UTI). The present study was planned to compare the performance of MALDI directly on urine samples with conventional urine culture and evaluate an algorithm using a combination of significant pyuria and MALDI directly on urine samples as a screening method for diagnosing UTI.

Materials and Methods

A total of 1000 urine samples from patients with symptoms suggestive of UTIs were analysed. Urine microscopy, urine culture and MALDI were performed simultaneously on all the samples.

Results

MALDI correctly identified the microorganisms in 73.83% monomicrobial samples. In culture showing a mixed growth of two and more than three organisms, MALDI was able to identify one microorganism in 27.58% and 15.78% of samples, respectively. There were no peaks by MALDI in 93.53% of 464 sterile samples. The sequential algorithm using urine microscopy and MALDI could correctly identify UTI in 66.23% cases.

Conclusion

MALDI can be utilised to rule out bacteriuria in >93% of sterile urine samples. The combination of significant pyuria and direct MALDI as screening method to diagnose UTI (whether monomicrobial or polymicrobial) was not found to be superior than using direct MALDI on urine samples alone.

Endemic fluoroquinolone-resistant Salmonellaenterica serovar Kentucky ST198 in northern India

Salmonellaenterica serovar Kentucky is an emergent human pathogen. Human infection with ciprofloxacin-resistant S. enterica Kentucky ST198 has been reported in Europe and North America as a consequence of travel to Asia/the Middle East. This is, to the best of our knowledge, the first study reporting the identification of this epidemic clone in India and South Asia.

Fecal carriage of carbapenem-resistant Enterobacteriaceae and risk factor analysis in hospitalised patients: A single centre study from India

PURPOSE

Carbapenem-resistant Enterobacteriaceae (CRE) have emerged and disseminated widely causing a variety of infections. In India, the carriage of CRE in hospitalised patients has not been well-studied. Therefore, we conducted the present study to observe gut carriage rate of CRE in patients admitted to our tertiary care hospital.

METHODS

A total of 232 faecal swabs collected from consecutive stool samples from admitted patients were inoculated on ChromID extended spectrum β-lactamase plates and members of Enterobacteriaceae family were subjected to antibiotic susceptibility as per the Clinical Laboratory Standards Institute guidelines. Polymerase chain reaction for blaVIM, blaKPC, blaIMPand blaNDM-1 genes was performed. CRE was identified if the isolates showed resistance to either imipenem or meropenem or showed the presence of resistant genes. Risk factors of patients with or without CRE colonisation were also analysed.

RESULTS

A total of 232 faecal swabs yielded 252 Enterobacteriaceae isolates, of which 49 isolates from 42 patients showed the presence of CRE (occurrence 42/232; 18.1%); 27 isolates from 22 patients carried blaNDM-1, whereas 20 isolates from 17 patients possessed blaVIMgene. No isolate was positive for blaKPCand blaIMPgenes. The CRE was common in both intensive care units (38.4%) and wards (46%) which may reflect the excessive use of broad-spectrum antibiotics in both these settings. The CRE was also found to have a significantly higher antimicrobial resistance as compared to non-CRE isolates. The logistic regression analysis of significance showed the presence of any indwelling device (P = 0.049) and nasogastric tube (P = 0.043) as independent risk factors for acquiring gut colonisation.

CONCLUSIONS

The study is the first from India to show high CRE carriage in patients admitted to a tertiary care centre and emphasises the need of strict antimicrobial stewardship implementation in hospitals to prevent dissemination of multidrug-resistant CRE.

Speciation, clinical profile & antibiotic resistance in Aeromonas species isolated from cholera-like illnesses in a tertiary care hospital in north India

Background & objectives:

Aeromonas species have been reported to cause various illnesses in humans such as wound infections, septicaemia, peritonitis and pneumonia. Their role in causation of cholera-like illness is also being increasingly recognized. This retrospective study was done to know the presence of Aeromonas as a cause of acute diarrhoea in a tertiary care hospital and to find the common species of Aeromonas causing diarrhoea and their antibiotic susceptibility patterns.

Methods:

Fifty isolates of Aeromonas were obtained over a period of 15 yr from 2000 to 2014 from patients of suspected acute gastroenteritis resembling cholera. Biotyping was done for 35 of these isolates available in culture collection, based on a panel of 13 biochemical reactions. Antibiogram was put up for all of these isolates by disk diffusion methods and interpreted according to the Clinical and Laboratory Standards Institute guidelines.

Results:

Of the 50 patients of Aeromonas-related acute gastroenteritis, 13 (26%) had typical features of cholera with rice water stools and severe dehydration. Eight patients (16%) had dysentery-like picture. One patient died of severe dehydration and septicaemia. The most common species were found to be Aeromonas caviae (34%) followed by Aeromonas veronii biovar veronii (29%), Aeromonas veronii biovar sobria (26%) and Aeromonas hydrophila (9%). All tested isolates were uniformly susceptible to cefepime, amikacin, azithromycin and meropenem; 14 per cent were susceptible to amoxicillin, 32 per cent to nalidixic acid, 60 per cent to co-trimoxazole, 54 per cent to ciprofloxacin, 60 per cent to ofloxacin, 74 per cent to chloramphenicol, 76 per cent to ceftriaxone, 74 per cent to cefotaxime, 88 per cent to gentamicin and 86 per cent to furoxone.

Interpretation & conclusions:

Aeromonas is an important, often neglected pathogen capable of causing a variety of gastrointestinal tract symptoms such as acute diarrhoea and dysentery and may even mimic cholera. It is, therefore, pertinent to recognize this pathogen as an important agent in the causation of severe diarrhoea.

Elizabethkingia miricola: A rare non-fermenter causing urinary tract infection

Elizabethkingia miricola (E. miricola) is a gram-negative non-fermentative bacterium which is rarely encountered. It is usually misidentified or considered as a contaminant in routine microbiology laboratories due to the limitations in conventional biochemical techniques. However, with the advent of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), the identification of non-fermenters has become easy and this has led to enhanced understanding of the clinical significance of these uncommonly isolated microorganisms. The genus Elizabethkingia has only two species E. meningoseptica and E. miricola. Both of these organisms are known to be multi-drug resistant and therefore, their accurate identification and antimicrobial susceptibility testing are necessary prior to the initiation of appropriate therapy. In the world literature till date, only 3 cases of sepsis caused by E. miricola have been reported. We present the first case of E. miricola association with urinary tract infection.

The 2002 Chandigarh cholera outbreak revisited: utility of MALDI-TOF as a molecular epidemiology tool

In July 2002, an outbreak of cholera occurred in north India with two separate geographical foci. Pulsed field gel electrophoresis (PFGE) was previously used in typing a representative sample of these isolates. This study evaluates the usefulness of MALDI-TOF as an epidemiological tool for typing Vibrio cholerae isolates in comparison with PFGE and Amplified fragment length polymorphisms (AFLP). Forty-six isolates of V. cholerae isolated from stool of patients affected in the July 2002 outbreak were typed using MALDI-TOF. To validate its utility, clinical and environmental isolates previously characterized by PFGE and AFLP were included for dendrogram analysis. All 46 isolates were correctly identified by MALDI-TOF to species level. Two distinct clades appeared on dendrogram using MALDI-TOF corresponding to the two geographical foci of the outbreak. For the study of evolution of organisms from environment, AFLP was superior as it clearly demarcated clinical and environmental isolates. The outbreak was not due to a single clone but due to multiple clones circulating simultaneously, as was seen with PFGE also.

SIGNIFICANCE AND IMPACT OF THE STUDY

MALDI-TOF appears to be a highly discriminatory, cost-effective and rapid epidemiological typing technique that can be used in the investigation of cholera outbreaks.

Biofilm formation capability of enterococcal strains causing urinary tract infection vis-a-vis colonisation and correlation with enterococcal surface protein gene

BACKGROUND

Data regarding differences in biofilm formation among urinary isolates of enterococci causing nosocomial infection versus asymptomatic colonisation is lacking. Conflicting data are available for the role of enterococcal surface protein (esp) gene in the development of enterococcal biofilms.

MATERIALS AND METHODS

A total of 50 (25 each of asymptomatic bacteriuria and urinary tract infection (UTI) isolates were collected from admitted patients who had nosocomial acquisition of enterococci in urine culture (≥105 cfu/ml). Biofilm assay was done by the quantitative adherence assay. Screening for esp gene was carried out by polymerase chain reaction, and confocal laser scanning microscopy was used to examine biofilms.

RESULTS

Out of 25 enterococcal isolates from asymptomatic patients, 9 (36%) isolates were found to be biofilm producers (6 weak [optical densities [OD]595 0.2] and three medium [OD595≥0.2 to595>0.5]). The esp gene was present in 30 (12 biofilm+, 18 biofilm-) isolates. Seventeen esp positive isolates were from asymptomatic cases whereas 13 were from UTI. However, we found that 100% of medium and strong biofilm producers were esp positive (P < 0.001). On comparing Enterococcus faecalis (n = 10) and E. faecium (n = 40) isolates, 70% of E. faecalis isolates were biofilm producers as compared to only 35% of E. faecium isolates (P > 0.05). The esp positivity was observed more in E. faecium isolates (65%) as compared to 40% in E. faecalis. Vancomycin-sensitive enterococcal and vancomycin-resistant enterococcal isolates and catheter-related and unrelated isolates showed similarity in biofilm production and esp positivity.

CONCLUSION

The esp gene is not compulsorily required to produce biofilm but when present may enhance the biofilm formation. We did not find any correlation between biofilm formation and the ability of the strain to cause symptomatic UTI be associated with catheters or vancomycin resistance.

Aerococcus Viridans: A Rare Pathogen Causing Urinary Tract Infection

Aerococci are Gram-positive cocci with colony morphology similar to viridans streptococci. Most often these isolates in clinical samples are misidentified and considered insignificant. However, with the use newer techniques like Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS), aerococci have been recognized as significant human pathogens capable of causing a diverse spectrum of infections. Among the different species of aerococci, Aerococcus urinae is the most common agent causing Urinary Tract Infection (UTI) followed by A. sanguinocola. Aerococcus viridans (A. viridans) have been reported rarely in urinary tract infections. The antimicrobial resistance in aerococci in terms of its intrinsic resistance and evolving resistance to penicillin and vancomycin has raised the concern for better understanding of this pathogen. We recently encountered two cases of nosocomial UTI caused by A. viridans which are being reported here.

Occurrence of blaNDM-₁ & absence of blaKPC genes encoding carbapenem resistance in uropathogens from a tertiary care centre from north India

Background & objectives:

Carbapenem resistance mediated by carbapenemases is increasingly being reported worldwide. This study was conducted to know the occurrence of important carbapenem resistance encoding genes in Gram-negative bacilli (GNB) causing complicated urinary tract infection (CUTI), and to look at the genetic diversity of these isolates.

Methods:

The study was carried out on 166 consecutive carbapenem resistant uropathogens (CRU) isolated from cases with CUTI during 2008 and 2012. Carbapenemase production was characterized phenotypically and polymerase chain reaction was used to detect bla_VIM, bla_IMP, bla_KPC, and bla_NDM-1. BOX- PCR was done on 80 randomly selected isolates for molecular typing.

Results:

The bla_VIM gene was present in 34 (43.6%), bla_IMP in five (6.4%) and none of the isolates from 2008 had bla_NDM-1 or bla_KPC genes. Among the isolates from 2012, bla_NDM-1 gene was present in 47 (53.4%), bla_VIM in 19 (24.4%), bla_IMP in one (1.1%) and none had bla_KPC. There were nine isolates during the two years which had multiple genes encoding carbapenemases; while 66 did not have any of the genes tested. Of the 80 isolates subjected to BOX-PCR, 58 could be used for analysis and showed, presence of multiple clusters of carbapenem resistant isolates and absence of a single dominant clone.

Interpretation & conclusions:

The bla_NDM-1 gene was absent in our isolates obtained during 2008 but was present amongst Enterobacteriaceae isolated in 2012. The bla_KPC gene was also not found. Nine isolates obtained during the two years had multiple genes encoding carbapenemases confirming the previous reports of emergence of GNB containing genes encoding multiple carbapenemases. Typing using BOX-PCR indicated that this emergence was not because of clonal expansion of a single strain, and multiple strains were circulating at a single point of time.

Pyonephrosis due to Chryseobacterium gleum: a first case report

Chryseobacterium spp are widely distributed in nature but data of their isolation from clinical samples is scanty. Here, we report the first case of AmpC producing C. gleum causing pyonephrosis in a patient having bilateral nephrolithiasis on double J (DJ) stent. The present isolate was resistant to vancomycin, erythromycin, clindamycin, carbapenems and ciprofloxacin and susceptible to tetracycline and minocycline. The patient was treated with tetracycline and recovered without the need for removal of the DJ stent. The environmental surveillance carried out to trace the nosocomial origin of the isolate was negative. Since antimicrobial susceptibility of this isolate is different from previous reports, we emphasise that in vitro susceptibility testing should be sought to choose optimal antimicrobial agents for these Nonfermentative Gram-Negative Bacilli (NFGNBs) with different susceptibility patterns.