Detection of blaCTX-M Extended Spectrum Beta-lactamase Producing Salmonella enterica Serotype Typhi in a Tertiary Care Centre

Unraveling the treasure trove of phytochemicals in mitigating the Salmonella enterica infection

Foodborne diseases triggered by various infectious micro-organisms are contributing significantly to the global disease burden as well as to increasing mortality rates. Salmonella enterica belongs to the most prevalent form of bacteria accountable for significant burden of foodborne illness across the globe. The conventional therapeutic approach to cater to Salmonella enterica-based infections relies on antibiotic therapy, but the rapid emergence of the antibiotic resistance strains of Salmonella sp. necessitates the development of alternative treatment and prevention strategies. In light of this growing concern, the scientific community is rigorously exploring novel phytochemicals harnessed from medicinally important plants as a promising approach to curb Salmonella enterica infections. A variety of phytochemicals belonging to alkaloids, phenols, flavonoid, and terpene classes are reported to exhibit their inhibitory activity against bacterial cell communication, membrane proteins, efflux pumps, and biofilm formation among drug resistant Salmonella strains. The present review article delves to discuss the emergence of antibiotic resistance among Salmonella enterica strains, various plant sources, identification of phytochemicals, and the current state of research on the use of phytochemicals as antimicrobial agents against Salmonella enterica, shedding light on the promising potential of phytochemicals in the fight against this pathogen.

Distribution of ß-Lactamase Genes Among Multidrug-Resistant and Extended-Spectrum ß-Lactamase-Producing Diarrheagenic Escherichia coli from Under-Five Children in Ethiopia

Purpose

Escherichia coli strains that produce extended-spectrum ß-lactamase (ESBL) and carbapenemase are among the major threats to global health. The objective of the present study was to determine the distribution of ß-lactamase genes among multidrug-resistant (MDR) and ESBL-producing Diarrheagenic E. coli (DEC) pathotypes isolated from under-five children in Ethiopia.

Patients and Methods

A cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia. It was a health-facility-based study and conducted between December 2020 and August 2021. A total of 476 under-five children participated in the study. DEC pathotypes were detected by conventional Polymerase Chain Reaction (PCR) assay. After evaluating the antimicrobial susceptibility profile of the DEC strains by disk diffusion method, confirmation test was done for ESBL and carbapenemase production. ß-lactamase encoding genes were identified from phenotypically ESBLs and carbapenemase positive DEC strains using PCR assay.

Results

In total, 183 DEC pathotypes were isolated from the 476 under-five children. Seventy-nine (43%, 79/183) MDR-DEC pathotypes were identified. MDR was common among enteroaggregative E. coli (EAEC) (58%, 44/76), followed by enterotoxigenic E. coli (ETEC) (44%, 17/39)) and enteroinvasive E. coli (EIEC) (30%, 7/23). Phenotypically, a total of 30 MDR-DEC pathotypes (16.4%, 30/183) were tested positive for ESBLs. Few ETEC (5.1%, 2/39) and EAEC (2.6%, 2/76) were carbapenemase producers. The predominant β-lactamase genes identified was blaTEM (80%, 24/30) followed by blaCTX-M (73%, 22/30), blaSHV (60%, 18/30), blaNDM (13%, 4/30), and blaOXA-48 (13%, 4/30). Majority of the ß-lactamase encoding genes were detected in EAEC (50%) and ETEC (20%). Co-existence of different β-lactamase genes was found in the present study.

Conclusion

The blaTEM, blaCTX-M, blaSHV, blaNDM, and blaOXA-48, that are associated with serious and urgent threats globally, were detected in diarrheagenic E. coli isolates from under-five children in Ethiopia. This study also revealed the coexistence of the β-lactamase genes.

Genomic Characterization of Salmonella enterica Resistant to Cephalosporin, Quinolones, And Macrolides

Salmonella enterica subsp. enterica (Salmonella), one of the most common causes of bacterial foodborne infections, causes salmonellosis, which is usually self-limiting. However, immunocompromised individuals and children often require antimicrobial therapy. The first line of treatment includes fluoroquinolones, to which Salmonella has emerging resistance worldwide. In fact, the WHO classified fluoroquinolone-resistant Salmonella as a high-priority pathogen. Salmonella carrying genes such as blaCTX and blaCMY can show resistance to cephalosporins which are also regularly used for treatment. This study focused on determining the antimicrobial resistance of 373 Salmonella isolates, collected from various foods, humans, and animals, as well as the environmental sludge between 2005 and 2020 in Türkiye. Phenotypic analysis of the resistance was determined by disk diffusion method. Isolates resistant to any of the following: ciprofloxacin, pefloxacin, azithromycin, and ceftriaxone were tested for the presence of quinolone, beta-lactamase, and/or macrolide resistance genes by PCR and gel electrophoresis. Five multi-drug-resistant isolates were then further whole genome sequenced and analyzed. More than 32% (n = 120) of the isolates showed resistance to fluoroquinolones by disc diffusion. A significant number of quinolone-resistant isolates are presented with mutated parC and gyrA. Furthermore, 42% (n = 106) of the isolates were resistant to azithromycin and 10% of them harbored mphA gene. On the bright side, only eight isolates showed resistance to ceftriaxone. Overall, we observed an increase in the number of isolates showing resistance to fluoroquinolones and azithromycin over the years and low resistance to ceftriaxone.

Phenotypic characterization and genome analysis of a novel Salmonella Typhimurium phage having unique tail fiber genes

Salmonella enterica serovar Typhimurium is a foodborne pathogen causing occasional outbreaks of enteric infections in humans. Salmonella has one of the largest pools of temperate phages in its genome that possess evolutionary significance for pathogen. In this study, we characterized a novel temperate phage Salmonella phage BIS20 (BIS20) with unique tail fiber genes. It belongs to the subfamily Peduovirinae genus Eganvirus and infects Salmonella Typhimurium strain (SE-BS17; Acc. NO MZ503545) of poultry origin. Phage BIS20 was viable only at biological pH and temperature ranges (pH7 and 37 °C). Despite being temperate BIS20 significantly slowed down the growth of host strain for 24 h as compared to control (P < 0.009). Phage BIS20 features 29,477-base pair (bp) linear DNA genome with 53% GC content and encodes for 37 putative ORFs. These ORFs have mosaic arrangement as indicated by its ORF similarity to various phages and prophages in NCBI. Genome analysis indicates its similarity to Salmonella enterica serovar Senftenberg prophage (SEStP) sequence (Nucleotide similarity 87.7%) and Escherichia virus 186 (~ 82.4% nucleotide similarity). Capsid genes were conserved however those associated with tail fiber formation and assembly were unique to all members of genus Eganvirus. We found strong evidence of recombination hotspot in tail fiber gene. Our study identifies BIS20 as a new species of genus Eganvirus temperate phages as its maximum nucleotide similarity is 82.4% with any phage in NCBI. Our findings may contribute to understanding of origin of new temperate phages.

Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae

Salmonella Typhimurium, a foodborne pathogen, is a major concern for food safety. Its MDR serovars of animal origin pose a serious threat to the human population. Phage therapy can be an alternative for the treatment of such MDR Salmonella serovars. In this study, we report on detailed genome analyses of a novel Salmonella phage (Salmonella-Phage-SSBI34) and evaluate its therapeutic potential. The phage was evaluated for latent time, burst size, host range, and bacterial growth reduction in liquid cultures. The phage stability was examined at various pH levels and temperatures. The genome analysis (141.095 Kb) indicated that its nucleotide sequence is novel, as it exhibited only 1-7% DNA coverage. The phage genome features 44% GC content, and 234 putative open reading frames were predicted. The genome was predicted to encode for 28 structural proteins and 40 enzymes related to nucleotide metabolism, DNA modification, and protein synthesis. Further, the genome features 11 tRNA genes for 10 different amino acids, indicating alternate codon usage, and hosts a unique hydrolase for bacterial lysis. This study provides new insights into the subfamily Vequintavirinae, of which SSBI34 may represent a new genus.

Antimicrobial Resistance in Salmonella Typhi Isolated From a Referral Hospital of Kathmandu, Nepal

Purpose:

The morbidity and mortality due to typhoid fever can be significantly reduced with the use of effective antibiotics. At present, fluoroquinolones, third generation cephalosporins, and azithromycin are widely used to treat typhoid fever. However, changing antibiotic susceptibility among Salmonella Typhi and Salmonella Paratyphi poses a particular challenge to the therapeutic management of enteric fever. The objective of this study was to assess the antibiotic susceptibility pattern of Salmonella Typhi isolates.

Patients and Methods:

A total of 706 blood specimens were collected from febrile patients attending the outpatient department of Kathmandu Model Hospital during June to September, 2018. The antibiotic susceptibility testing for 11 different antibiotics (nalidixic acid, ciprofloxacin, ofloxacin, levofloxacin, cefixime, ceftriaxone, cefotaxime, azithromycin, cotrimoxazole, chloramphenicol, and amoxicillin) was performed by disk diffusion method. Furthermore, minimum inhibitory concentration (MIC) values of ciprofloxacin, ofloxacin, and azithromycin were determined by agar dilution method. Mutation at gyrA ser83 associated with reduced susceptibility to fluoroquinolones was determined by PCR-RFLP.

Results:

Out of 706 blood samples, 6.94% (n = 49) were culture positive for Salmonella enterica (S. Typhi, n = 46). It was revealed that 97.8% S. Typhi isolates were susceptible to conventional first-line antibiotics (ampicillin, chloramphenicol, and cotrimoxazole), 97.3% to cephalosporins and 95.7% to azithromycin. S. Typhi were either resistant or intermediately susceptible to fluoroquinolones: 97.8% to ciprofloxacin, 91.3% to ofloxacin, and 89.1% to levofloxacin. The MIC of ciprofloxacin, ofloxacin, and azithromycin for S. Typhi ranged from 0.008 to 32, 0.03 to 16, and 2 to 8 μg/mL, respectively. Out of 46 S. Typhi isolates, 44 (95.65%) had gyrA ser83 mutation.

Conclusion:

Fluoroquinolones have poor activity against Salmonella Typhi. The trends of increasing azithromycin MIC value among S. Typhi might limit its use for the treatment of typhoid fever. Effectiveness of conventional first-line antibiotics in vitro suggests considering their clinical use after large-scale studies.

Molecular Detection of gyrA Gene in Salmonella enterica serovar Typhi Isolated from Typhoid Patients in Baghdad

BACKGROUND AND OBJECTIVE

Typhoid fever is endemic in most countries, causing major public health problems with high morbidity and mortality, the resistance of Salmonella enterica serovar Typhi (S. Typhi) towards antimicrobials is recently increased. The aim was to detect the harboring gyrA gene in Typhi Salmonella enterica serovar.

MATERIALS AND METHODS

Twenty Salmonella enterica serovar Typhi isolates were obtained from the Teaching laboratories of the medical city in Baghdad, the isolates were obtained from blood specimens from typhoid patients. Colonies of Salmonella enterica serovar Typhi appeared on CHROM agar and Xylose Lysine Deoxycholate Agar (XLD) as light mauve to mauve-colored and as red with black center colonies, respectively. Polymerase Chain Reaction (PCR) technique was used to detect the presence of the gyrA gene within the twenty isolates with specific primer.

RESULTS

All twenty isolates show the highest resistance rates to Cefazolin 18 (90%), Ciprofloxacin 16 (80%), and Nalidixic acid 15 (75%), while it shows highest sensitivity rates to Cefepime 18 (90%) and Tobramycin 16 (80%) antibiotics. The MIC values show equal to or more than breakpoint of Nalidixic acid and Ciprofloxacin were 15 (75%) and 16 (80%) isolates, respectively.

CONCLUSION

PCR results showed the presence of gyrA gene (488 bp) in 14 (70%) of isolates (isolate number 1, 2, 3, 4, 7, 8, 9, 10, 12, 13, 14, 15, 18 and 19). On the other hand, 6(30%) isolates (isolate numbers 5, 6, 9, 11, 16, 17, and 20) don't harbor the gyrA gene.

A systematic review of antimicrobial resistance of typhoidal Salmonella in India

Background & objectives:

The temporal trends in the development of antimicrobial resistance (AMR) among Salmonella Typhi and Salmonella Paratyphi in India have not been systematically reported. We aimed to systematically review the temporal AMR trends (phenotypic and molecular mechanisms) in bacterial isolates from patients with enteric fever over two decades in India.

Methods:

To identify trends in AMR in India, resistance patterns among 4611 individual S. Typhi isolates and 800 S. Paratyphi A isolates, reported from 1992 to 2017 in 40 publications, were analysed. Molecular resistance determinants were extracted from 22 publications and also reviewed in accordance with the PRISMA guidelines. Articles were sourced using a predefined search strategy from different databases.

Results:

The analyses suggested that multidrug-resistant (MDR) enteric fever was declining in India and being replaced by fluoroquinolone (FQ) resistance. Mutations in gyrA and parC were key mechanisms responsible for FQ resistance, whereas MDR was largely driven by resistance determinants encoded on mobile genetic elements (plasmids, transposons).

Interpretation & conclusions:

The results reflect the effect of antimicrobial pressure which has been driving AMR in typhoidal Salmonella in India. Understanding these trends is important in planning future approaches to therapy, which serve as a baseline for assessment of the impact of new typhoid conjugate vaccines against these resistant organisms.

A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid

BACKGROUND

The temporal and spatial change in trends of antimicrobial resistance (AMR) in typhoid have not been systematically studied, and such information will be critical for defining intervention, as well as planning sustainable prevention strategies.

METHODOLOGY AND FINDINGS

To identify the phenotypic trends in AMR, 13,833 individual S. Typhi isolates, reported from 1973 to 2018 in 62 publications, were analysed to determine the AMR preponderance over time. Separate analyses of molecular resistance determinants present in over 4,000 isolates reported in 61 publications were also conducted. Multi-drug resistant (MDR) typhoid is in decline in Asia in a setting of high fluoroquinolone resistance while it is on the increase in Africa. Mutations in QRDRs in gyrA (S83F, D87N) and parC (S80I) are the most common mechanisms responsible for fluoroquinolone resistance. Cephalosporin resistant S. Typhi, dubbed extensively drug-resistant (XDR) is a real threat and underscores the urgency in deploying the Vi-conjugate vaccines.

CONCLUSION

From these observations, it appears that AMR in S. Typhi will continue to emerge leading to treatment failure, changes in antimicrobial policy and further resistance developing in S. Typhi isolates and other Gram-negative bacteria in endemic regions. The deployment of typhoid conjugate vaccines to control the disease in endemic regions may be the best defence.