Molecular Characterization of Extensively Drug Resistant Salmonella Enterica Serovar Typhi Clinical Isolates from Lahore, Pakistan

Community engagement: the missing piece in solving the puzzle of XDR-typhoid spread in Pakistan

Typhoid has been a major infectious health threat for the masses in Pakistan with increasing antimicrobial resistance, socio-economic decline, and environmental challenges. Since 2019, the percentage of cases has reduced with the implementation of Typhoid Conjugate Vaccine (TCV) program but reports of widened geographical spread particularly as aftermath of flooding in 2022 and resistance to Azithromycin or Meropenem in adult population are a matter of serious concern. Now is the right time to reconsider whether strategies like mass immunization or health infrastructure development solely can combat the hazards of Extensively Drug-Resistant (XDR)-Typhoid. Public health policies developed due to COVID-19, such as incorporating all stakeholders especially the public through community engagement, may provide a collaborative effort to lessen the prevailing threat of antibiotic resistance.

Comprehensive analysis of β-lactam resistant non-typhoidal Salmonella Isolates: Phenotypic and genotypic insights from clinical samples in Japan

OBJECTIVE

This study examines β-lactam-resistant non-typhoidal Salmonella isolates using phenotypic and genotypic analyses to elucidate resistance mechanisms and epidemiological characteristics.

METHODS

A total of 1663 clinical Salmonella spp. isolates were collected (1994-2016), with 122 exhibiting β-lactam resistance, confirmed via antimicrobial susceptibility testing. Resistance mechanisms were further explored through genotypic analysis by whole genome sequencing, plasmid characterization, and phylogenomic investigations.

RESULTS

All isolates were resistant to at least one β-lactam. Resistance to third-generation cephalosporins was notable, while carbapenem resistance was rare (0.8%). High resistance was observed for minocycline (36.9%) and sulfamethoxazole-trimethoprim (28.7%), whereas resistance to fluoroquinolones (3.3%-5.7%), aminoglycosides (0.8%-8.2%), and tigecycline (8.2%) was low. All isolates remained susceptible to fosfomycin, and 21.3% exhibited multidrug resistance. Genotypic analysis identified diverse serotypes and sequence types, with S. Typhimurium and ST19 being predominant. The most common β-lactamase gene was blaTEM, followed by blaCARB-2, with significant correlations between β-lactam and aminoglycoside resistance genes. Plasmid analysis revealed a high prevalence of plasmid carriage, with IncFII(S) and IncFIB(S) being predominant, strongly associated with antimicrobial resistance genes. Phylogenetic analysis provided insights into the global dissemination of Salmonella, particularly those carrying mcr-9, while clustering analysis revealed shared genetic patterns among isolates sourced from different hosts, highlighting the potential for cross-species transmission.

CONCLUSIONS

These findings underscore the complex interplay of resistance mechanisms and emphasize the need for integrated surveillance and intervention strategies to combat antimicrobial resistance in Salmonella, reinforcing the necessity for ongoing public health efforts.

Pan-genome analysis and drug repurposing strategies for extensively drug-resistant Salmonella Typhi: Subtractive genomics and e-pharmacophore approaches

In the current study, we presented the genome sequence and taxonomic classification of the new extensively drug-resistant (XDR) Salmonella enterica serovar Typhi strain JRCGR-ST-AK02. Its genome size was found to be 4,780,534 bp, containing 4864 genes. Taxonomic classification was performed based on the Average Nucleotide Identity (ANI), Genome-to-Genome Distance Calculator (GGDC) and Average Amino Acid Identity (AAI) analysis. Pan-genome analysis revealed 34,4915 core genes, which are predominantly involved in general functions and carbohydrate metabolism. We used a subtractive genomics approach and identified the PocR protein as a drug target. Its 3D structure was built using homology modeling, and an e-pharmacophore hypothesis was created using its binding site. The pharmacophore hypothesis was screened against FDA-approved ligands library and a total of 2018 out 9392 drugs were selected for molecular docking. Cangrelor and Pentagastrin presented docking scores of -9.503 and -9.081 kcal/mol, respectively. The binding dynamics of these promising FDA-approved drugs were further confirmed through 200 ns molecular dynamics simulation, highlighting their stable and strong interactions with the PocR protein. Our study highlights the potential of Cangrelor and Pentagastrin for repurposing against XDR Salmonella Typhi. By identifying these drugs as promising candidates, we pave the way for new treatments for XDR Salmonella Typhi infections.

Doripenem, Ertapenem, and Meropenem Sensitivity in Salmonella Typhi: A Cross-Sectional Study From Pakistan

Background Salmonella Typhi (S. Typhi) is increasingly resistant to multiple antibiotics, posing a challenge in treatment, particularly in multidrug-resistant (MDR) cases. Carbapenems, including doripenem, ertapenem, and meropenem, have been considered last-resort options. This study evaluates the effectiveness of these carbapenems against S. Typhi isolates in a clinical setting in Peshawar, Pakistan. Objective To assess the effectiveness of the carbapenem antibiotics, doripenem, ertapenem, and meropenem, against S. Typhi. Methods This study collected data from blood cultures of patients diagnosed with S. Typhi infections at the Hayatabad Medical Complex in Peshawar, Pakistan for two years: from January 1, 2022, to December 31, 2023. Sensitivity testing was performed using the disk diffusion method in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines. The analysis examined the sensitivity rates of the three antibiotics and compared their effectiveness. Results A total of 626 S. Typhi isolates were tested. Only 11.98% of the isolates were sensitive to doripenem, while 88.02% were resistant to it. In contrast, 35.5% of the isolates responded to ertapenem, with 64.5% being resistant. Meropenem showed the highest efficacy, with 42.7% of the isolates demonstrating sensitivity. These findings highlight the growing challenge of managing multidrug-resistant (MDR) S. Typhi infections, especially in regions where resistance to carbapenems is becoming prevalent. Conclusion Meropenem proved to be more effective against S. Typhi compared to doripenem and ertapenem. The study emphasizes the need for ongoing monitoring of resistance patterns and the exploration of alternative or combination treatment options. These findings have immediate clinical implications for empiric therapy choices and highlight the urgent need for antibiotic stewardship programs in endemic regions.

Combatting extensively drug-resistant Salmonella: a global perspective on outbreaks, impacts, and control strategies

Antibiotic resistance in typhoid fever poses a critical public health problem due to the emergence of extensively drug-resistant (XDR) Salmonella, resulting in prolonged illness and treatment failure. Salmonella enterica serovar Typhi is the most predominant among all serotypes and can acquire resistance. The emergence of XDR Salmonella in various regions globally, particularly Pakistan, presents a concerning trend. However, limited data availability impedes a comprehensive understanding of the outbreaks and hinders the development of real-time solutions. Here, we have provided an updated overview of the current outbreaks of XDR Salmonella in epidemic and endemic regions. Treatments of XDR Salmonella infections are challenging, as there are records of treatment failure in humans and animals. However, intensive prevention techniques can be implemented pending the advent of novel antibiotics. Emphasis on antimicrobial stewardship and frequent surveillance of the pathogen should be made to keep track of potential outbreaks in both human and animal populations. Although progress is being made to combat XDR Salmonella within some regions, a unified and efficient effort on an international scale is required to curtail the XDR outbreak before it escalates and leads us back to the pre-antibiotic era.

Exploring the antimicrobial efficacy of Manuka honey against multidrug-resistant and extensively drug-resistant Salmonella Typhi causing septicemia in Pakistan

Aim: To determine the efficacy of manuka honey against multidrug-resistant (MDR) and extensively drug-resistant (XDR) clinical strains of Salmonella Typhi.Materials & methods: Clinical isolates were processed using the Bactec blood culture system, identification and antibiogram by Vitek 2 and antibiotic resistance genes through polymerase chain reaction (PCR). Microbroth dilution assays evaluated the antibacterial activity of manuka honey.Results: MDR and XDR-S. Typhi was susceptible to azithromycin. These strains carried the H58, gyrA, gyrB, blaCTX-M-15 , and blaTEM-1 genes. At 100% honey, the zone of inhibition for MDR (15-23 mm) and XDR (15-24 mm) strains. 18/50 MDR and 14/50 XDR strains inhibited at 3.125 v/v% killed at 6.25 v/v% concentration respectively.Conclusion: Manuka honey could be an alternative option for treating S. Typhi infections.

Effectiveness of Oral Azithromycin in Treating Enteric Fever: A Hospital-Based Study on Pediatric Patients

Introduction Enteric fever is prevalent in underdeveloped and developing countries. It is caused by Salmonella Typhi, which has developed resistance over the years to commonly used antimicrobials. Meropenem is an effective treatment for all complicated and uncomplicated extensively drug-resistant (XDR) bacteria, but it is administered intravenously, three times daily, by infusion, and it is quite expensive for the patient. Oral azithromycin is shown by some authors to be effective in extensively drug-resistant enteric fever. Material and methods This retrospective cross-sectional study was conducted in the outpatient department of Lady Reading Hospital Medical Teaching Institution, Peshawar. The duration of the study was one year. Data was collected after approval from the hospital's Ethical and Research Committee. All pediatric patients meeting the inclusion criteria for extensively drug-resistant enteric fever were included. Data on patient demographics, blood culture and laboratory results, treatment given, and effectiveness were documented in a specialized proforma. Statistical Package for Social Sciences (SPSS) version 23 (IBM Corp., Armonk, NY, US) was used for data analysis. Results Out of the total 106 patients, 72 (67.9%) were male and 34 (32.1%) were female. The mean age was 7.51 ± 2.75 years, with a range of 1 to 15 years. Among them, 66 (62.3%) had anemia (hemoglobin less than 11 grams per deciliter for under 5 years and 11.5 for 5-15 years old children), with a mean hemoglobin level of 10.6 ± 1.53 grams per deciliter (g/dl), ranging from 7.2 to 13.8 g/dl. Thrombocytopenia was found in 14 (13%) patients. The mean platelet count was 317 x 103 ± 164 cells per microliter, with a range of 61 x 103 to 834 x 103 cells per liter. The mean total leukocyte count was 9.71x 103 ± 4.321 cells per microliter, with a range of 2.01 x 103 to 30.40 x103 cells per microliter. However, leucopenia was seen in only 5 (4.7%) patients. In 98.1% of cases, azithromycin was found to be effective in treating enteric fever caused by extensively drug-resistant Salmonella. Conclusion Azithromycin is effective in treating extensively drug-resistant enteric fever. It can be confidently used in patients with no or mild complications with extensively drug-resistant enteric fever. Good compliance and complete dosage should be followed to avoid resistance to this drug. Blood cultures should always be sent when prescribing antibiotics, especially when suspecting enteric fever.

The Salmonella typhi Cell Division Activator Protein StCAP Impacts Pathogenesis by Influencing Critical Molecular Events

Conserved molecular signatures in multidrug-resistant Salmonella typhi can serve as novel therapeutic targets for mitigation of infection. In this regard, we present the S. typhi cell division activator protein (StCAP) as a conserved target across S. typhi variants. From in silico and fluorimetric assessments, we found that StCAP is a DNA-binding protein. Replacement of the identified DNA-interacting residue Arg34 of StCAP with Ala34 showed a dramatic (15-fold) increase in Kd value compared to the wild type (Kd 546 nm) as well as a decrease in thermal stability (10 °C shift). Out of the two screened molecules against the DNA-binding pocket of StCAP, eltrombopag, and nilotinib, the former displayed better binding. Eltrombopag inhibited the stand-alone S. typhi culture with an IC50 of 38 μM. The effect was much more pronounced on THP-1-derived macrophages (T1Mac) infected with S. typhi where colony formation was severely hindered with IC50 reduced further to 10 μM. Apoptotic protease activating factor1 (Apaf1), a key molecule for intrinsic apoptosis, was identified as an StCAP-interacting partner by pull-down assay against T1Mac. Further, StCAP-transfected T1Mac showed a significant increase in LC3 II (autophagy marker) expression and downregulation of caspase 3 protein. From these experiments, we conclude that StCAP provides a crucial survival advantage to S. typhi during infection, thereby making it a potent alternative therapeutic target.

Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay

Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.