Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.

A suitcase laboratory was used for 16S rRNA amplicon sequencing to assess microbial water quality in the holy Bagmati River, Kathmandu, Nepal. SourceTracker analysis and Volcano plots revealed that microbial communities in the downstream part of the river were mainly contributed by untreated sewage. Seasonal variability in the sewage microbiome was reflected in the downstream river water quality. The bacterial genera Acidovorax, Geobacillus and Caulobacter predominated in the upstream sites, while genera containing putative human pathogens and gut bacteria, such as Clostridium, Prevotella, Arcobacter, Lactobacillus, Enterococcus and Streptococcus become prominent in the downstream sites. Marker gene qPCR assays for total bacteria, total coliforms, Human E. coli, Arcobacter butzleri and Vibrio cholerae confirmed the sequencing data trends. Even though basic sanitation provision is nowadays near universal in Nepal, our findings show how inadequate wastewater management may turn an urban river into an open sewer, which poses a public health risk.

Background. Bacterial contamination in intensive care units is an important risk factor associated with increasing incidences of nosocomial infections. This study was conducted to study the bacterial colonization on commonly touched objects of intensive care units and antibiotic resistance pattern of bacterial isolates. Methods. This study was conducted in different intensive care units of Manipal Teaching Hospital, Pokhara, Nepal. A total of 235 swabs were collected from surfaces of bed rails, monitors, door handles, IV stands, telephone sets, nursing stations, medicine trolleys, sphygmomanometers, wash basin taps, dressing drums, stethoscopes, pulse oximeters, ventilators, defibrillators, and stretchers. Isolation, identification, and antibiotic susceptibility tests of the bacteria were performed following standard microbiological techniques. Results. Of 235 samples, bacterial growth was observed in 152 samples. A total of 90 samples of Staphylococcus aureus were isolated from 235 samples. Most of the sampling sites included in this study were found contaminated with S. aureus. The highest number of S. aureus was cultured from the surface of bed rails. Of the total S. aureus isolates, 54.4 (49/90) were methicillin-resistant Staphylococcus aureus (MRSA). Vancomycin resistance was detected among 8.1 MRSA isolates (4/49). Acinetobacter species were the commonest Gram-negative bacterial isolate. Conclusion. Bacterial contamination of the objects/instruments of the ICU was recorded to be high. The most common contaminating bacteria were S. aureus with a high percentage of MRSA and emergence of VRSA. Periodic microbiological surveillance, detection of contaminated sites, and effective decontamination methods would minimize the colonization by potential pathogens and their transmission.

Klebsiella pneumoniae is a common opportunistic pathogen causing a wide range of infections; pneumonia, urinary tract infection, bacteremia, and liver abscesses. It infects primarily immunocompromised and immunocompetent individuals. It presents itself as an antibiotic-resistant bacterium, especially for third-generation cephalosporins and carbapenems, creating serious global challenges. Therefore, this cross-sectional study was conducted in B & B Hospital, Lalitpur to screen the distribution of carbapenem resistance K. pneumoniae through ertapenem and to assess the minimum inhibitory concentration of imipenem for screened carbapenem resistance K. pneumoniae. From 3447 different clinical samples collected according to standard guidelines, K. pneumoniae was identified using standard microbiological techniques; staining and a panel of biochemical tests. The antibiotic susceptibility test of the isolates was performed by the Kirby-Bauer disc diffusion method as per CLSI 2018 guidelines. The screening of carbapenem resistance was assessed by using ertapenem disc and the MIC of imipenem for carbapenem resistance and intermediate was performed using an Epsilometer. A total of 85 K. pneumoniae were identified and their antibiotic susceptibility test revealed that ceftriaxone was the least effective antibiotic. The number of MDR, carbapenem-resistant and intermediate isolates was 51, 46, and 3, respectively. The MIC of imipenem through an Epsilometer from ertapenem resistant and intermediate revealed that 31, 5, and 13 isolates were resistant, intermediate, and sensitive respectively. These findings showed the inconsistency in the detection of carbapenem-resistant isolates in routine microbiology laboratories and further support the other tests for the detection of carbapenem resistance as suggested by CLSI.

Background Klebsiella pneumoniae is a ubiquitous Gram-negative, non-motile, encapsulated bacterium that resides in the mucosal surfaces of mammals and the environment such as soil, water, etc. Clinically, it is also associated with many infections and conditions that are aggravated by the acquisition of multidrug-resistant genes. MethodsThis descriptive study was conducted to find out the incidence of Klebsiella pneumoniae in different clinical samples and their antibiotic susceptibility pattern at B & B Hospital, Lalitpur from 12 June 2022 to 11 September 2022. The samples were cultured on MacConkey agar, and standard microbiological techniques were used to confirm the presence of K. pneumoniae. Antimicrobial susceptibility tests were performed using the Kirby-Bauer Disk Diffusion method.ResultsOf the 1967 different clinical samples, culture positivity was observed in 361 samples. Among these, total number of Klebsiella pneumoniae was 150 (41.55%) and from the urine samples exclusively, 63 (42%) Klebsiella pneumoniae were isolated. The most susceptible and resistant antibiotics were gentamicin and ciprofloxacin respectively. Among the isolates, 85 (56.66%) isolates were multi-drug resistant in which 69 (87.34%) isolates were resistant to carbapenem.Conclusions The diversified infections with a growing number of multi-drug resistant Klebsiella pneumoniae present a major public health concern. The limited availability of effective antibiotics emphasizes the prudent use of available antibiotics and the importance of regular national-wide surveillance of multi-drug resistance patterns.