Molecular Docking of Multidrug Resistant Klebsiella pneumoniae from River Water of Klang Valley, Malaysia

Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions

Antimicrobial resistance has been a serious and complex issue for over a decade. Although research on antimicrobial resistance (AMR) has mainly focused on clinical and animal samples as essential for treatment, the AMR situation in aquatic environments may vary and have complicated patterns according to geographical area. Therefore, this study aimed to examine recent literature on the current situation and identify gaps in the AMR research on freshwater, seawater, and wastewater in Southeast Asia. The PubMed, Scopus, and ScienceDirect databases were searched for relevant publications published from January 2013 to June 2023 that focused on antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARGs) among water sources. Based on the inclusion criteria, the final screening included 41 studies, with acceptable agreement assessed using Cohen's inter-examiner kappa equal to 0.866. This review found that 23 out of 41 included studies investigated ARGs and ARB reservoirs in freshwater rather than in seawater and wastewater, and it frequently found that Escherichia coli was a predominant indicator in AMR detection conducted by both phenotypic and genotypic methods. Different ARGs, such as blaTEM, sul1, and tetA genes, were found to be at a high prevalence in wastewater, freshwater, and seawater. Existing evidence highlights the importance of wastewater management and constant water monitoring in preventing AMR dissemination and strengthening effective mitigation strategies. This review may be beneficial for updating current evidence and providing a framework for spreading ARB and ARGs, particularly region-specific water sources. Future AMR research should include samples from various water systems, such as drinking water or seawater, to generate contextually appropriate results. Robust evidence regarding standard detection methods is required for prospective-era work to raise practical policies and alerts for developing microbial source tracking and identifying sources of contamination-specific indicators in aquatic environment markers.

Characterization of a Lytic Bacteriophage and Demonstration of Its Combined Lytic Effect with a K2 Depolymerase on the Hypervirulent Klebsiella pneumoniae Strain 52145

Klebsiella pneumoniae is a nosocomial pathogen. Among its virulence factors is the capsule with a prominent role in defense and biofilm formation. Bacteriophages (phages) can evoke the lysis of bacterial cells. Due to the mode of action of their polysaccharide depolymerase enzymes, phages are typically specific for one bacterial strain and its capsule type. In this study, we characterized a bacteriophage against the capsule-defective mutant of the nosocomial K. pneumoniae 52145 strain, which lacks K2 capsule. The phage showed a relatively narrow host range but evoked lysis on a few strains with capsular serotypes K33, K21, and K24. Phylogenetic analysis showed that the newly isolated Klebsiella phage 731 belongs to the Webervirus genus in the Drexlerviridae family; it has a 31.084 MDa double-stranded, linear DNA with a length of 50,306 base pairs and a G + C content of 50.9%. Out of the 79 open reading frames (ORFs), we performed the identification of orf22, coding for a trimeric tail fiber protein with putative capsule depolymerase activity, along with the mapping of other putative depolymerases of phage 731 and homologous phages. Efficacy of a previously described recombinant K2 depolymerase (B1dep) was tested by co-spotting phage 731 on K. pneumoniae strains, and it was demonstrated that the B1dep-phage 731 combination allows the lysis of the wild type 52145 strain, originally resistant to the phage 731. With phage 731, we showed that B1dep is a promising candidate for use as a possible antimicrobial agent, as it renders the virulent strain defenseless against other phages. Phage 731 alone is also important due to its efficacy on K. pneumoniae strains possessing epidemiologically important serotypes.

Multidrug-Resistant Gram-Negative Bacteria and Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae from the Poultry Farm Environment

The indiscriminate use and overuse of various antibiotics have caused the rapid emergence of antibiotic-resistant bacteria (ARB) in poultry products and the surrounding environment, giving rise to global public health issues. This study aimed to determine the prevalence of multidrug-resistant (MDR) Gram-negative bacteria (GNB) found in the environment of poultry farms and to evaluate the risk of contamination in these farms based on multiple antibiotic resistance (MAR) index values. Soil and effluent samples were collected from 13 poultry farms. The VITEK 2 system was used for bacterial identification and susceptibility testing of the isolates. The identified Gram-negative isolates were Acinetobacter spp., Aeromonas spp., Enterobacter spp., Klebsiella pneumoniae, Proteus spp., Providencia spp., Pseudomonas spp., and Sphingomonas paucimobilis. The results showed that Enterobacter spp., Aeromonas spp., and Providencia spp. exhibited the highest MDR rates and MAR indices; 14% of K. pneumoniae isolates (3/21 isolates) were resistant to 13 antibiotics and found to be extended-spectrum β-lactamase (ESBL)-producing bacteria. As for the tested antibiotics, 96.6% of the isolates (28/29 isolates) demonstrated resistance to ampicillin, followed by ampicillin-sulbactam (55.9% [33/59 isolates]) and cefazolin (54.8% [57/104 isolates]). The high percentage of MDR bacteria and the presence of ESBL-producing K. pneumoniae strains suggested the presence of MDR genes from the poultry farm environment, which poses an alarming threat to the effectiveness of the available antibiotic medicines to treat infectious diseases. Therefore, the use of antibiotics should be regulated and controlled, while studies addressing One Health issues are vital for combating and preventing the development and spread of ARB. IMPORTANCE The occurrence and spread of ARB due to high demand in poultry industries are of great public health concern. The widespread emergence of antibiotic resistance, particularly MDR among bacterial pathogens, poses challenges in clinical treatment. Some pathogens are now virtually untreatable with current antibiotics. However, those pathogens were rarely explored in the environment. In alignment with the concept of One Health, it is imperative to study the rate of resistance in the environment, because this domain plays an important role in the dissemination of bacteria to humans, animals, and other environmental areas. Reliable data on the prevalence of MDR bacteria are crucial to curb the spread of bacterial pathogens that can cause antimicrobial-resistant infections.

Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia

Objectives

This study profiled the prevalence of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-EC) in the community and compared their resistome and genomic profiles with isolates from clinical patients through whole-genome sequencing.

Methods

Fecal samples from 233 community dwellers from Segamat, a town in southern Malaysia, were obtained between May through August 2018. Putative ESBL strains were screened and tested using antibiotic susceptibility tests. Additionally, eight clinical ESBL-EC were obtained from a hospital in the same district between June through October 2020. Whole-genome sequencing was then conducted on selected ESBL-EC from both settings (n = 40) for pan-genome comparison, cluster analysis, and resistome profiling.

Results

A mean ESBL-EC carriage rate of 17.82% (95% CI: 10.48%– 24.11%) was observed in the community and was consistent across demographic factors. Whole-genome sequences of the ESBL-EC (n = 40) enabled the detection of multiple plasmid replicon groups (n = 28), resistance genes (n = 34) and virulence factors (n = 335), with no significant difference in the number of genes carried between the community and clinical isolates (plasmid replicon groups, p = 0.13; resistance genes, p = 0.47; virulence factors, p = 0.94). Virulence gene marker analysis detected the presence of extraintestinal pathogenic E. coli (ExPEC), uropathogenic E. coli (UPEC), and enteroaggregative E. coli (EAEC) in both the community and clinical isolates. Multiple blaCTX-M variants were observed, dominated by blaCTX-M-27 (n = 12), blaCTX-M-65 (n = 10), and blaCTX-M-15 (n = 9). The clinical and community isolates did not cluster together based on the pan-genome comparison, suggesting isolates from the two settings were clonally unrelated. However, cluster analysis based on carried plasmids, resistance genes and phenotypic susceptibility profiles identified four distinct clusters, with similar patterns between the community and clinical isolates.

Conclusion

ESBL-EC from the clinical and community settings shared similar resistome profiles, suggesting the frequent exchange of genetic materials through horizontal gene transfer.