Jatan Bahadur Sherchan

Clinical Epidemiology and Molecular Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli in Nepal: Characteristics of Sequence Types 131 and 648

ABSTRACT Recently, CTX-M-type extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli strains have emerged worldwide. In particular, E. coli with O antigen type 25 (O25) and sequence type 131 (ST131), which is often associated with the CTX-M-15 ESBL, has been increasingly reported globally; however, epidemiology reports on ESBL-producing E. coli in Asia are limited. Patients with clinical isolates of ESBL-producing E. coli in the Tribhuvan University teaching hospital in Kathmandu, Nepal, were included in this study. Whole-genome sequencing of the isolates was conducted to analyze multilocus sequence types, phylotypes, virulence genotypes, O25b-ST131 clones, and distribution of acquired drug resistance genes. During the study period, 105 patients with ESBL-producing E. coli isolation were identified, and the majority (90%) of these isolates were CTX-M-15 positive. The most dominant ST was ST131 (n = 54; 51.4%), followed by ST648 (n = 15; 14.3%). All ST131 isolates were identified as O25b-ST131 clones, subclone H30-Rx. Three ST groups (ST131, ST648, and non-ST131/648) were compared in further analyses. ST648 isolates had a proportionally higher resistance to non-β-lactam antibiotics and featured drug-resistant genes more frequently than ST131 or non-ST131/648 isolates. ST131 possessed the most virulence genes, followed by ST648. The clinical characteristics were similar among groups. More than 38% of ESBL-producing E. coli isolates were from the outpatient clinic, and pregnant patients comprised 24% of ESBL-producing E. coli cases. We revealed that the high resistance of ESBL-producing E. coli to multiple classes of antibiotics in Nepal is driven mainly by CTX-M-producing ST131 and ST648. Their immense prevalence in the communities is a matter of great concern.

Cyclospora Infection among School Children in Kathmandu, Nepal: Prevalence and Associated Risk Factors

Background: The intestinal coccidian protozoa Cyclospora cayetanensis has emerged as an important cause of parasitic diarrhea among children living in developing countries. This study aimed to determine the prevalence of Cyclospora among the school children of Kathmandu with reference to various associated risk factors. Methodology: A total of five hundred and seven stool samples from students between the age of 3–14 years, studying in 13 different schools in Kathmandu were collected during the study period (May–November, 2014) and processed at the Public Health Research Laboratory, Institute of Medicine, Kathmandu, Nepal. A modified acid fast staining technique (Kinyoun’s method) was used to detect oocyst of Cyclospora from the formal-ether concentrated stool samples. Results: Cyclospora was detected in 3.94% (20/507) of the stool samples examined. The prevalence was found to be highest among the students in the 3–5 year age group i.e. 10.15% (13/128), peaking during the rainy season (June–August). The detection rate was found to be significantly higher (p < 0.05) among children presenting with diarrheal symptoms, household keeping livestock and consumers of raw vegetables/fruits, showing a prevalence of 10.57% (11/104), 10.11% (9/89) and 7.25% (14/193) respectively. Conclusion: Consumption of untreated drinking water, fresh produce (raw fruits/vegetables) without proper washing and the presence of livestock at home were found to be predisposing factors for higher susceptibility of infection due to Cyclospora. This finding confirms the existence of a public-health issue with potentially serious consequences whereby children can be infected through exposure to oocysts in contaminated food and water and get ill as a result.

Comparative Genome Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Sequence Type 131 Strains from Nepal and Japan.

The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia. ABSTRACT The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted whole-genome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region. IMPORTANCE The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia.

Molecular and Clinical Epidemiology of Salmonella Paratyphi A Isolated from Patients with Bacteremia in Nepal

Little is known about the epidemiology of typhoid and paratyphoid fever in Nepal. We aimed to elucidate the molecular and clinical epidemiology of Salmonella Paratyphi A in Nepal. Isolates were collected from 23 cases of bacteremia due to S. Paratyphi A between December 2014 and October 2015. Thirteen patients (57%) were male, and the median age was 21 years. None of the patients had an underlying chronic disease. All S. Paratyphi A isolates were sensitive to ampicillin, trimethoprim/sulfamethoxazole, ceftriaxone, and chloramphenicol. All isolates were resistant to nalidixic acid and were categorized as intermediately susceptible to levofloxacin. Phylogenetic analysis revealed close relatedness among the isolates, including several clonal groups, suggesting local spread. Patients with bacteremia due to S. Paratyphi A in Kathmandu, Nepal, were relatively young and nondebilitated. Improving control of S. Paratyphi infections should focus on effective infection control measures and selection of empirical therapy based on current resistance patterns.

Prevalence of group A genotype human rotavirus among children with diarrhoea in Nepal, 2009–2011.

Background: Rotavirus as a causative agent of childhood diarrhea is known to cause serious illness among children less than 5 years of age. This study examined the epidemiology of rotavirus disease burden and diversity of G and P genotypes of rotavirus in Nepal. Methods: Stool samples were tested for rotavirus by Enzyme Immuno Assay and Group A rotaviruses were detected by using both ELISA and RT-PCR in 2718 samples between 2009 and 2011. Results: Rotavirus was more frequently detected among inpatients (28.5%) than outpatients (15.2%). Over the three-year study period, 653 (24.4%) cases were positive for rotavirus by ELISA. Genotyping by RT-PCR was done on 638 samples. The most prevalent genotype was G12P [6] (60.4%). Mixed infections were not uncommon (14% in 2009, 29% in 2010 an 7% in 2011). However, 41 were partially typed and 23 were completely untyped over the study period. Conclusions: This study highlights the rotavirus disease burden and diversity of rotavirus strains circulating in Nepal. Continued sentinel surveillance will provide useful information to policy makers with regard to rotavirus vaccine introduction.

Correction for Miyoshi-Akiyama et al., “Comparative Genome Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Sequence Type 131 Strains from Nepal and Japan”

[This corrects the article DOI: 10.1128/mSphere.00289-16.].