Distribution of Integrons and Phylogenetic Groups among Enteropathogenic Escherichia coli Isolates from Children <5 Years of Age in Delhi, India

Multidrug resistance-encoding gene in Citrobacter freundii isolated from healthy laying chicken in Blitar District, Indonesia

Background and Aim: The increasing prevalence of resistance (MDR) of Enterobacteriaceae in Indonesia has caused concern regarding human health. Citrobacter freundii reportedly targets the gastrointestinal tract of animals and is a common cause of foodborne diseases associated with diarrhea, peritonitis, meningitis, brain abscess, bacteremia, and urinary tract infection. This study aimed to estimate the prevalence of MDR and the presence of Class 1 integron-encoding genes in C. freundii isolates obtained from cloacal swabs of healthy laying chickens in Blitar district, Indonesia. Materials and Methods: One hundred and sixty-five cloacal swab samples were collected from 33 farms in Blitar over a period of 4 months. Standard microbiological techniques such as bacterial culture in MacConkey agar, Simmons citrate agar, and triple sugar iron agar and biochemical tests such as the indole test were performed to identify the isolates. The antibiotic sensitivity patterns of C. freundii isolates were determined by the disk diffusion method, and MDR-encoding genes (Class 1 integron) were detected by polymerase chain reaction (PCR). Results: Out of 165 cloacal swab samples, 7 (4.24%) were positive for C. freundii. Citrobacter freundii was highly resistant to erythromycin (71.43%) and moderately to streptomycin, tetracycline, and trimethoprim-sulfamethoxazole (all 42.86%); however, it showed low resistance to ampicillin (28.57%). All isolates were found to exhibit MDR. Only 1 (14.29%) of the seven C. freundii isolates harbored a Class 1 integron gene. This study revealed that Class 1 integron-encoding genes have a low prevalence in C. freundii isolated from healthy laying chickens in Blitar, Indonesia. Conclusion: Poultry animals can play a role in the transmission of resistance genes to humans due to the MDR of Enterobacteriaceae, including C. freundii in the intestines.

Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico

Escherichia coli is a leading cause of human enteric diseases worldwide. The rapid and accurate causal agent identification to a particular source represents a crucial step in the establishment of safety and health measures in the affected human populations and would thus provide insights into the relationship of traits that may contribute for pathogen persistence in a particular reservoir. The objective of the present study was to characterize over two hundred E. coli strains from different isolation sources in Mexico by conducting a correspondence analysis to explore associations with the detected phylogenetic groups. The results indicated that E. coli strains, recovered from distinct sources in Mexico, were classified into phylogroups B1 (35.8%), A (27.8%), and D (12.3%) and were clustered to particular clades according to the predicted phylogroups. The results from correspondence analysis showed that E. coli populations from distinct sources in Mexico, belonging to different phylogroups, were not dispersed randomly and were associated with a particular isolation source. Phylogroup A was strongly associated with human sources, and the phylogroup B1 showed a significant relationship with food sources. Additionally, phylogroup D was also related to human sources. Phylogroup B2 was associated with herbivorous and omnivorous mammals. Moreover, common virulence genes in the examined E. coli strains, assigned to all phylogroups, were identified as essential markers for survival and invasion in the host. Although virulence profiles varied among the detected phylogroups, E. coli strains belonging to phylogroup D, associated with humans, were found to contain the largest virulence gene repertoire conferring for persistence and survival in the host. In summary, these findings provide fundamental information for a better characterization of pathogenic E. coli, recovered from distinct isolation sources in Mexico and would assist in the development of better tools for identifying potential transmission routes of contamination.

Analysis of Nucleotide Sequences Similarity and Protein Prediction of Some Resistance Genes in Escherichia coli Isolated from Iraqi Patients with Urinary Tract Infections

Antibiotic resistance leads to a dramatic increase in the morbidity and mortality caused by infectious diseases. Even though estimates vary widely, the economic cost of antimicrobial-resistant bacteria is on a rise. The current aimed to identify the antimicrobial resistance of Escherichia coli (E. coli). In fact, this study focused on the recent deep-learning methods (sequencing) to investigate E. coli antibiotic resistance and their protein sequences. To evaluate antibiotic resistance, the sequencing method could be considered the method of choice. The E. coli was identified by either specific biochemical tests or polymerase chain reaction (PCR) using the 16S rRNA gene. The results of aadA1 gene sequences demonstrated 10 nucleic acid substitutions throughout, as compared to the reference NCBI database (MG385063). Out of the 10 nucleic acid substitutions, 9 missense effects were observed. While the dfrA1 gene sequences illustrated 20 nucleic acid substitutions throughout, compared to the reference NCBI database (KY706080), out of the 20 nucleic acid substitutions, 8 missense effects were observed. Furthermore, the sul1 gene sequences displayed 20 nucleic acid substitutions throughout, in comparison with the reference NCBI database (CP069561), and out of the 20 nucleic acid substitutions, 12 missense effects were detected. The cat1 gene sequences showed 14 nucleic acid substitutions throughout, compared to the reference NCBI database (NC017660), and out of the 14 nucleic acid substitutions, 8 missense effects were observed. The precise point (Missense) mutation in four genes (aadA1, dfrA1, sul1, and cat1) in the expected sequence is interpreted to be the target site of a site-specific recombination mechanism that led to antibiotics resistance in E. coli isolates.

A Study on Multidrug-Resistant Escherichia coli Clinical Isolates from Different Hospitals in Greater Cairo

The biological fitness cost of antibiotic resistance is a key parameter in determining the rate of appearance and spread of antibiotic-resistant bacteria in Egypt. Our study aimed to investigate the prevalence of antibiotic resistance among Escherichia coli clinical isolates from Greater Cairo area hospitals. A total of 537 clinical isolates were recovered from samples of urine, diarrheal specimen, pus, wound culture, gastric wound, blood, drain culture, sputum, high vaginal swab, abscess, amniotic fluid, ventilator, burn swab, splenic drain culture, and unknown site of infection during different seasons. All isolates were subjected to phenotypic and genotypic susceptibility testing for colistin, nitrofurantoin, fosfomycin, and trimethoprim, quinolones, and β-lactam resistance. Our results revealed that 42.7% of the isolates harbored at least one resistance encoding gene, 10% harboring 2, 0.6% harboring 3, and 0.85% harboring 4 resistance-encoding genes. PCR reported the prevalence of resistance genes as follows: bla-SHV 13.4%, mcr-1 0.6%, qnr-A 23.8%, fos-A 1.06%, nfs-A 3.6%, and dfr-A 25.5%. We reported that three isolates carried the mcr-1 gene encoding colistin resistance from three different hospitals. Upon performing sequencing and phylogenetic analysis on the three positive mcr-1 isolates (MT890587, MT890588, and MT890589), the three isolates showed 100% identity with themselves, with some strains from Egypt and Japan, and 99.9% identity with an isolate from China.

Integron mediated antimicrobial resistance in diarrheagenic Escherichia coli in children: in vitro and in silico analysis

The exchange of genes between bacterial chromosome and plasmid(s) and their integration into integrons are mainly responsible for acquisition and dissemination of antibiotic resistance. We investigated the role of integrons and their underlying molecular mechanisms leading to development of adaptability in E. coli and eventual resistance to antimicrobials. Escherichia coli isolates (n = 120); including 40 diarrheagenic isolates, an even number of isolates from cases other than diarrhea, and equal number of isolates from healthy children recovered from fresh stool samples were used for identification of integron genes and gene cassettes. The association of integrons with antibiotic resistance was assayed before phylogenetic analysis. DNA sequence analysis revealed class 1 and 2 integrons in 55.83% and 21.66% isolates, respectively. The integron presence was found significantly associated with the probability of antibiotic resistance in E. coli; the association being highest with class 1 integron. Modelling and molecular docking along with molecular dynamics simulation analyses found ceftriaxone and amoxicillin as potential inhibitors of dihydrofolate reductase (DHFR). The class 1 integrons of these pathogenic isolates can serve as prospective therapeutic targets using specific silencing strategies and combinational antimicrobial therapy. The findings may be useful for the development of a potent and versatile drug for DHFR inhibition.

Characterization of Antimicrobial Susceptibility, Extended-Spectrum β-Lactamase Genes and Phylogenetic Groups of Enteropathogenic Escherichia coli Isolated from Patients with Diarrhea

Objectives

Infectious diarrhea is one of the most common causes of pediatric death worldwide and enteropathogenic Escherichia coli (EPEC) is one of the main causes. There are 2 subgroups of EPEC, typical and atypical, based on the presence or absence of bundle forming pili (bfp), of which atypical EPEC is considered less virulent, but not less pathogenic. Antimicrobial resistance towards atypical EPEC among children is growing and is considered a major problem. In this study the pattern of antibiotic resistance in clinical isolates was determined.

Methods

Using 130 isolates, antibiotic resistance patterns and phenotypes were assessed, and genotypic profiles of extended spectrum β-lactamase (ESBL) production using disc diffusion and PCR was carried out. Phylogenetic groups were analyzed using quadruplex PCR.

Results

There were 65 E. coli isolates identified as atypical EPEC by PCR, among which the highest antibiotic resistance was towards ampicillin, followed by trimethoprim-sulfamethoxazole, and tetracycline. Multidrug resistance was detected in 44.6% of atypical EPEC isolates. Around 33% of isolates were determined to be extended spectrum β-lactamase producers, and in 90% of isolates, genes responsible for ESBL production could be detected. Moreover, the majority of atypical EPEC strains belonged to Group E, followed by Groups B1, B2 and C.

Conclusion

High rates of multidrug resistance and ESBL production among atypical EPEC isolates warrant periodical surveillance studies to select effective antibiotic treatment for patients. It is considered a critical step to manage antibiotic resistance by avoiding unnecessary prescriptions for antibiotics.

Molecular Characterization and Antimicrobial Resistance of Enteropathogenic Escherichia coli in Children from Ahvaz, Iran

Background: Enteropathogenic Escherichia coli (EPEC) is one of the most important pathogens among young children worldwide. Both eae and bfp genes have been used to identify EPEC strains and categorize them into typical and atypical strains. They may be an emerging pathogen in both developing and developed countries. Objectives: This study was primarily conducted to assess the epidemiology, drug resistance, and β-lactamase distribution of EPEC, as well as the detection of efa1/lifA in atypical strains. Methods: A total of 251 E. coli strains isolated from children with diarrhea were evaluated for their EPEC pathotype by PCR for the presence of eae, stx1, stx2, and bfp genes. Serogrouping with polyvalent antisera was performed to confirm EPEC strains. Atypical EPEC-containing samples were evaluated for the efa1/lifA gene. EPEC isolates were assessed to recognize the antibiotic resistance and screened to detect extended-spectrum β-lactamases (ESBLs). Results: Enteropathogenic E. coli strains were detected in 17 (6.78%) of E. coli isolates by PCR. The prevalence of typical and atypical strains was determined at 35.3% and 64.7%. All strains were completely susceptible to colistin, imipenem, and meropenem. The prevalence of blaCTX-M and blaTEM genes was calculated at 70.58% and 58.82%, respectively. Conclusions: Enteropathogenic E. coli isolates are completely sensitive to carbapenems, and precise therapeutic strategies are required to prevent the spread of these beta-lactamase genes among diarrheagenic E. coli.

Aetiology and outcome of acute diarrhoea in children with severe acute malnutrition: a comparative study

OBJECTIVE

To compare the microbiological profile, clinical course and outcome of acute diarrhoea in children aged <5 years having severe acute malnutrition (SAM) with those of children having normal nutritional status.

DESIGN

Cross-sectional comparative study.

SETTING

Tertiary-care hospital catering mainly to the urban poor of East Delhi, India.

PARTICIPANTS

Children aged <5 years (n 140; seventy with SAM (cases) and seventy with normal anthropometry (controls)) with acute diarrhoea (duration < 14 d). Stool samples were collected for conventional culture, microscopy, acid-fast staining, rotavirus and Cryptosporidium antigen detection, and subtyping of diarrhoeagenic Escherichia coli (DEC). We followed-up these children for persistent diarrhoea and subsequent diarrhoeal episode in the next 3 months.

RESULTS

Rotavirus was detected in six (9 %) cases and in fifteen (21 %) controls (P = 0·03; OR = 0·34; 95 % CI 0·12, 0·94). DEC was isolated significantly more in cases compared with controls (93 v. 64 %; P < 0·001; OR = 7·25; 95 % CI 2·57, 20·4). Cryptosporidium was detected in seven (10 %) cases and five (7 %) controls. Total duration of diarrhoea and percentage change in weight after resolution of diarrhoea were comparable between cases and controls. At 3-month follow-up, number of subsequent episodes of diarrhoea and persistent diarrhoea were comparable between the two groups.

CONCLUSIONS

Rotavirus was found significantly less frequently, whereas DEC was detected more frequently in children with SAM in comparison to non-malnourished children. To further reduce diarrhoea-related mortality, preventive and therapeutic interventions need to be designed against organisms causing diarrhoea in children with SAM.

Typical and atypical enteropathogenic Escherichia coli in children with acute diarrhoea: Changing trend in East Delhi

Background

Worldwide around 2 million deaths occur every year due to diarrhoeal illnesses among children less than 5 years of age. Among diarrhoeagenic Escherichia coli, Enteropathogenic E. coli (EPEC) is highly prevalent in both community and hospital settings and is one of the main causes of persistent diarrhea in children in developing countries. EPEC remains underdiagnosed in India due to lack of conventional tools for identification.

Methods

We in this study investigated the prevalence and regional variation of EPEC in paediatric population suffering from diarrhoea in East Delhi, India. Two hundred stool samples were collected from children, aged between 0.5 and 5 years, with acute diarrhoea. E. coli were identified by conventional tests and PCR.

Results

We observed 7% atypical EPEC (aEPEC) and 2.5% typical EPEC (tEPEC), with an overall 9.5% EPEC prevalence amongst total samples. E. coli phylogenetic group A was the predominant. The most common age group affected was 6–23 months with common symptoms being vomiting, watery diarrhoea and severe dehydration. High drug resistance pattern was observed in EPEC isolates.

Conclusion

The study depicts a changing trend of aEPEC over tEPEC in children less than 5 years with diarrhoea, an emerging drug resistant enteropathogen and a public health concern demanding monitoring and surveillance.

Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea

BACKGROUND

Escherichia coli strains include both commensal and virulent clones distributed in different phylogenetic groups. Antimicrobial resistance is an increasingly serious public health threat at the global level and integrons are important mobile genetic elements involved in resistance dissemination. This paper aims to determine the phylogenetic groups and presence of class 1 (intl1) and 2 (intl2) integrons in E. coli clinical isolates from children with diarrhoea, and to associate these characteristics with their antimicrobial resistance.

METHODS

Phylogeny and presence of integrons (intl1 and intl2) were analysed by PCR and amplicon sequencing in 70 E. coli isolates from children with and without diarrhoea (35 of each group) from Sinaloa, Mexico; these variables were analysed for correlation with the antimicrobial resistance profile of the isolates.

RESULTS

The most frequent phylogroups were A (42.9%) and B2 (15.7%). The E. coli isolates from children with diarrhoea were distributed in all phylogroups; while strains from children without diarrhoea were absent from phylogroups C, E, and clade I. The 17.1% of the isolates carried integrons (15.7% intI1 and 1.4% intI2); 28.6% of the isolates from children with diarrhoea showed the class 1 integron. Strains of phylogroup A showed the highest frequency of integrons (33.3%). The association of multidrug resistance and the presence of integrons was identified in 58.3% of strains isolated from children with diarrhoea included in phylogroups A and B2. The sequence analysis of intl1 and intl2 showed silent point mutations and similarities with plasmids of some APEC and AIEC strains.

CONCLUSION

Commensal E. coli strains are potential disseminators of antimicrobial resistance, and the improvement in the use of antimicrobials to treat childhood diarrhoea is essential for the control of such resistance.

Changing paradigm of antibiotic resistance amongst Escherichia coli isolates in Indian pediatric population

Antimicrobial resistance happens when microorganisms mutates in manners that render the drugs like antibacterial, antiviral, antiparasitic and antifungal, ineffective. The normal mutation process is encouraged by the improper use of antibiotics. Mutations leading to quinolone resistance occur in a highly conserved region of the quinolone resistance-determining region (QRDR) of DNA gyrAse and topoisomerase IV gene. We analyzed antibiotic resistant genes and single nucleotide polymorphism (SNP) in gyrA and parC genes in QRDR in 120 E. coli isolates (both diarrheagenic and non-pathogenic) recovered from fresh stool samples collected from children aged less than 5 years from Delhi, India. Antibiotic susceptibility testing was performed according to standard clinical and laboratory standards institute (CLSI) guidelines. Phylogenetic analysis showed the clonal diversity and phylogenetic relationships among the E. coli isolates. The SNP analysis depicted mutations in gyrA and parC genes in QRDR. The sul1 gene, responsible for sulfonamide resistance, was present in almost half (47.5%) of the isolates across the diseased and healthy samples. The presence of antibiotic resistance genes in E. coli isolates from healthy children indicate the development, dissemination and carriage of antibiotic resistance in their gut. Our observations suggest the implementation of active surveillance and stewardship programs to promote appropriate antibiotic use and minimizing further danger.

Interrelationship between tetracycline resistance determinants, phylogenetic group affiliation and carriage of class 1 integrons in commensal Escherichia coli isolates from cattle farms

BACKGROUND

Carriage of antibiotic-resistant foodborne pathogens by food production animals is one of many contributors to treatment failure in health care settings, and it necessitates an integrated approach to investigate the carriage of resistant pathogens harboring integrons in food-producing animals.

METHODS

Escherichia coli isolates with reduced susceptibility to tetracycline antibiotics (n = 92) were tested for associations between carriage of class1 integrons, phylogenetic group affiliation and tetracycline resistance determinants using the MIC method, PFGE analysis, PCR and sequencing.

RESULTS

Phylogroups B1 and A were the most common (58.7 and 19.6%, respectively), followed by groups D (20.7%) and B2 (1.1%). All isolates carried at least one of the tet genes examined. In addition, 88 (95.7%) of all tetracycline-resistant isolates carried tet(A) or tet(B), while 47 (51.1%) and 41 (44.6%) harbored only tet(A) or tet(B), respectively. Likewise, isolates harboring these genes had a higher chance (P < 0.05) of carrying class 1 integrons. Of the tested isolates, 38 (41.3%) carried the intI1 gene. Classical integrons with complete genes (sul1 and qacE∆1) at the 3'-CS were recognized in 27 isolates. PCR screening and subsequent sequencing demonstrated that 84.2% (32/38) of the intI1-positive isolates harbored resistance gene cassettes. Overall, seven gene cassettes were identified, either solely or combined with another gene cassette. The most common gene was aadA1 (10 isolates), followed by a combination of aadA1-dfrA1 (seven isolates), aadA1-dfrA12 (six isolates) and aadA1-aadA2-dfrA12 (three isolates). Genetic typing using PFGE showed minimum clonal relatedness with 28 different clusters and 12-25 discernible DNA fragments.

CONCLUSIONS

This study brings new insight into the relationships between the presence of integrons, phylogenetic group association and characteristics of tetracycline antibiotic resistance determinants in commensal E. coli strains.

A study of virulence and antimicrobial resistance pattern in diarrhoeagenic Escherichia coli isolated from diarrhoeal stool specimens from children and adults in a tertiary hospital, Puducherry, India

BACKGROUND

Emergence of atypical enteropathogenic Escherichia coli (EPEC) and hybrid E. coli (harboring genes of more than one DEC pathotypes) strains have complicated the issue of growing antibiotic resistance in diarrhoeagenic Escherichia coli (DEC). This ongoing evolution occurs in nature predominantly via horizontal gene transfers involving the mobile genetic elements like integrons notably class 1 integron. This study was undertaken to determine the virulence pattern and antibiotic resistance among the circulating DEC strains in a tertiary care center in south of India.

METHODS

Diarrhoeal stool specimens were obtained from 120 children (< 5 years) and 100 adults (> 18 years), subjected to culture and isolation of diarrhoeal pathogens. Conventional PCR was performed to detect 10 virulence and 27 antimicrobial resistance (AMR) genes among the E. coli isolated.

RESULTS

DEC infection was observed in 45 (37.5%) children and 18 (18%) adults, among which [18 (40%), 10 (10%)] atypical EPEC was most commonly detected followed by [6 (13.3%), 4 (4%)] ETEC, [5 (11.1%) 2 (2%)] EAEC, [(3 (6.6%), 0 (0%)] EIEC, [3 (6.6%), 0 (0%] typical EPEC, and [4 (8.8%), 1 (1%)] STEC, and no NTEC and CDEC was detected. DEC co-infection in 3 (6.6%) children, and 1(1%) adult and sole hybrid DEC infection in 3 (6.6%) children was detected. The distribution of sulphonamide resistance genes (sulI, sulII, and sulIII were 83.3 and 21%, 60.41 and 42.1%, and 12.5 and 26.3%, respectively) and class 1 integron (int1) genes (41.6 and 26.31%) was higher in DEC strains isolated from children and adults, respectively. Other AMR genes detected were qnrS, qnrB, aac(6')Ib-cr, dhfr1, aadB, aac(3)-IV, tetA, tetB, tetD, catI, blaCTX, blaSHV, and blaTEM. None harbored qnrA, qnrC, qepA, tetE, tetC, tetY, ermA, mcr1, int2, and int3 genes.

CONCLUSIONS

Atypical EPEC was a primary etiological agent of diarrhea in children and adults among the DEC pathotypes. Detection of high numbers of AMR genes and class 1 integron genes indicate the importance of mobile genetic elements in spreading of multidrug resistance genes among these strains.

Identification and efficacy of glycine, serine and threonine metabolism in potentiating kanamycin-mediated killing of Edwardsiella piscicida

We previously showed that glucose potentiated kanamycin to kill multidrug-resistant Edwardsiella piscicida through activation of the TCA cycle. However, whether other regulatory mechanism is involved requires further investigation. By quantitative proteomics technology, iTRAQ, we systematically mapped the altered proteins in the presence of glucose and identified 94 differentially expressed proteins. The analysis of the altered proteins by pathways, amino acid biosynthesis and metabolism were enriched. And the most significantly altered eight amino acids tyrosine, phenylalanine, valine, leucine, isoleucine, glycine, serine and threonine were investigated for their potentiation of kanamycin to kill EIB202, where glycine, serine and threonine showed the strongest efficacy than the others. The combinations of glycine and serine or glucose with glycine, serine or threonine had the best effects. Moreover, pyruvate dehydrogenase, α-ketoglutarate dehydrogenase and succinate dehydrogenase activities were increased as well as the proton motive force (PMF) and intracellular kanamycin. Finally, inhibitors that disrupt PMF production abolished the potentiation. These results shed light on the mechanism of how glucose promoting the amino acids biosynthesis and metabolism to potentiate kanamycin to kill antibiotic-resistant bacteria. More importantly, our results suggested that adjusting amino acid biosynthesis and metabolism might be a strategy to become phenotypic resistance to antibiotics in bacteria.

SIGNIFICANCE

Tackling antibiotic resistance is an emerging issue in current years. Despite the efforts made toward developing new antibiotics, the progress is still lagged behind expectation. Novel strategies are required. The use of metabolite to revert antibiotic resistant is highly appreciated in recent years due to the less toxicity, more economic and high efficacy. As a continued study of our previous report on glucose potentiating kanamycin to kill antibiotic-resistant bacteria. The current study further expands the previous discovery on the mechanism of how glucose potentiate this effect. This result provides more basis on the action of glucose in reverting antibiotic resistance. And more importantly, we may derive more metabolites other than glucose to manage antibiotic resistance.