Objective: To analyze drug resistance patterns in Salmonella isolates from Khyber Pakhtunkhwa (KPK) based on three-year surveillance data from Tehsil Head Quarter (THQ) Hospital, Dogar Central, Kurram, Pakistan.
Study design: It is a retrospective and descriptive study based on laboratory surveillance data.
Place and duration of study: The study was conducted at the THQ Hospital Laboratory. Data were extracted from laboratory sites located in KPK province from January 2019 to December 2022.
Methodology: Blood culture and sensitivity data (2019-2024) were reviewed for resistance trends in S. Typhi and S. Paratyphi A.
Result: A total of 621 isolations were reported, including 562 S. Typhi and 59 S. Paratyphi A. Ciprofloxacin (100%), ceftriaxone (92%), cefixime (92%), ampicillin (95%), chloramphenicol (90%), and trimethoprim-sulfamethoxazole (81%) were the antibiotics against which S. Typhi showed high resistance. S. Typhi showed minimal resistance to azithromycin (0.2%) and continued to be susceptible to meropenem (0% resistance). Conversely, S. Paratyphi A isolates showed 100% fluoroquinolone resistance but no resistance to first-line medications.
Conclusion: In Pakistan, the emergence of extensively drug-resistant (XDR) S. Typhi is a serious treatment challenge. Urgent needs include increasing immunization coverage, regulating sensible antibiotic usage, and strengthening surveillance.

Enteric fever, Salmonella Typhi, Salmonella Paratyphi A, Resistance, Antimicrobial stewardship.

Enteric fever is a systemic infection caused by Salmonella enterica serovars Typhi and Paratyphi A. XDR Salmonella typhi strains are defined as isolates resistant to first-line agents (ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole), fluoroquinolones, and third-generation cephalosporins, leaving only limited therapeutic options such as azithromycin and carbapenems. It remains a major public health concern in South Asia, particularly in Pakistan.[1,2] Globally, an estimated 9 to 12 million cases of enteric fever occur annually, with the highest incidence in South Asian countries, where inadequate sanitation, limited access to clean water, and overburdened healthcare systems contribute to ongoing transmission.[1,2]

In Pakistan, typhoid fever has become a common challenge, specifically affecting children and young adults and causing substantial morbidity, mortality, and economic burden. In 2016, the first outbreak of XDR typhoid was reported in Karachi, raising global alarm due to resistance against fluoroquinolones and third-generation cephalosporins.[3,4] Since that initial outbreak, XDR S. Typhi strains have rapidly disseminated to multiple provinces, including Sindh, Punjab, and KPK, making Pakistan one of the epicenters of this public health crisis.[5] The extensive spread of these resistant strains has challenged traditional treatment methods and highlighted the urgent need for effective surveillance and preventative measures. Historically, enteric fever was effectively managed with first-line antibiotics, such as chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole. However, by the late 1980s, multidrug resistance (MDR), defined as resistance to all three of these agents, emerged and quickly spread across endemic regions.[6] This shift forced clinicians to adopt fluoroquinolones and third-generation cephalosporins as standard therapy in the 1990s and early 2000s.[7] Unfortunately, the overuse and misuse of these antibiotics led to widespread resistance and severely limited their effectiveness. Alarmingly, resistance rates to fluoroquinolones now exceed 90% in many regions of Pakistan, and resistance to cephalosporins has escalated in parallel, resulting in the emergence of XDR strains.[8,9] Azithromycin and carbapenems remain the last reliable therapeutic options for XDR typhoid.[8,9] However, increased reports of decreased susceptibility and sporadic resistance to azithromycin are concerning because they increase the risk of incurable infections. However, rising reports of reduced susceptibility and sporadic resistance to azithromycin are alarming, as they heighten the risk of untreatable infections if carbapenem resistance emerges.

These developments highlight the importance of continuous surveillance and rational antibiotics stewardship and public health interventions, which include expanded vaccination programs. Against this backdrop, the present study analyzes three-year surveillance data from THQ Hospital Dogar Laboratory, which focuses on resistance patterns in S. Typhi and S. Paratyphi A isolated from KPK. This study aims to determine the antimicrobial resistance pattern of Salmonella typhi isolates.

Study design: This was a retrospective, descriptive study based on laboratory surveillance data. The analysis was conducted using routinely collected microbiology records from blood culture specimens, focusing on antimicrobial resistance trends in Salmonella Typhi and Salmonella Paratyphi A isolates. Retrospective laboratory-based designs are considered reliable for assessing antimicrobial resistance patterns in high-burden settings. The data collected from Nasser Ullah Baber Memorial Hospital provides a large sample size and minimizes recall bias.

Setting: The study was carried out at THQ Hospital Central Kurram Dogar Laboratory, which serves patients across both urban and rural areas. For this analysis, data were extracted from laboratory sites, including Naseer Ullah Baber, located in KPK province between January 2019 and December 2022. KPK is a region with a high reported burden of enteric fever15 and surveillance data from this province are critical for understanding emerging resistance trends.

Sample size and isolate selection: A total of 621 non-duplicate blood culture isolates of Salmonella enterica were included in the study. Among these, 562 (90.5%) were identified as S. Typhi and 59 (9.5%) as S. Paratyphi A. Only the first isolate per patient episode was included to avoid duplication and overestimation of resistance rates. Demographic details (age, gender, and geographic distribution) were not included in this dataset, as the primary focus was on antimicrobial resistance.

Microbiological Identification and antimicrobial susceptibility testing (AST): Blood culture samples were processed according to standard microbiological protocols. Isolate identification was carried out by using conventional biochemical methods and confirmed by automated systems when required. API (Analytical Profile Index) is an automated identification system widely used in clinical microbiology laboratories. It consists of miniaturized biochemical tests arranged in a strip format, which are inoculated with a bacterial suspension. After incubation, results are interpreted either visually or through an automated reader and compared against a large database for species-level identification. API is valued for its reliability, standardization, and rapid turnaround compared to conventional biochemical methods. AST was performed by using the disk diffusion and minimum inhibitory concentration (MIC) methods as per the Clinical and Laboratory Standards Institute (CLSI) guidelines.[7] Quality control was performed using corresponding ATCC control strains to validate each antibiotic tested in the AST process. The antibiotics tested included ciprofloxacin, ampicillin, cefixime, ceftriaxone, chloramphenicol, trimethoprim-sulfamethoxazole, azithromycin, and meropenem, representing both first-line and advanced therapeutic options. Breakpoints for resistance were interpreted according to CLSI criteria (CLSI, 2024, M100, 34th edition).

Data Management and Analysis: Resistance percentages were calculated for each antimicrobial agent by dividing the number of resistant isolates by the total number of isolates tested. Resistance profiles were stratified by species (S. Typhi vs S. Paratyphi A). Trends were assessed descriptively across the five-year study period. Data cleaning was performed to ensure accuracy, with exclusion of incomplete or inconclusive AST results. Statistical software was not required for advanced modeling, as the study was designed to provide surveillance-based descriptive resistance patterns rather than inferential comparisons.

Three-year surveillance period (2019-2022), a total of 621 non-duplicate blood culture isolates of Salmonella enterica were identified from patients in KPK of THQ Hospital Dogar and Naseer Ullah Baber Memorial Hospital. Of these, the majority were S. Typhi (n= 562; 90.5%), while S. Paratyphi A (n=59; 9.5%) accounted for a smaller proportion. This distribution is consistent with regional and national trends, where S. Typhi continues to predominate as the primary cause of enteric fever in Pakistan.[5,9]

Antimicrobial resistance patterns: The antimicrobial susceptibility profiles of the isolates are summarized in Table 1. S. Typhi: Resistance was alarmingly high against several antibiotic classes.

Complete resistance (100%) was observed to ciprofloxacin, while very high resistance was documented to ampicillin (95%), ceftriaxone (92%), chloramphenicol (90%), and trimethoprim-sulfamethoxazole (81%). Notably, azithromycin resistance was extremely rare (0.2%), and no resistance was detected against meropenem (0%). S. Paratyphi A: In contrast, S. Paratyphi A remained susceptible to most first-line and cephalosporin antibiotics, though complete resistance (100%) was observed to ciprofloxacin. These findings confirm the widespread presence of XDR S. Typhi in KPK, while S. Paratyphi A remains relatively susceptible to conventional therapies except fluoroquinolones.[3,5,9]

Figure 1: Antimicrobial resistance trends in S. Typhi (2019-2022, KPK)

Table 1: Antimicrobial resistance rates in S. Typhi and S. Paratyphi A isolates from Khyber Pakhtunkhwa, Pakistan (2019-2022)

Trend analysis: A review of resistance trends over the study period revealed the following patterns:

S. Typhi: Demonstrated persistently high resistance to fluoroquinolones and cephalosporins throughout 2019–2022, with no evidence of declining trends. Resistance to first-line antibiotics, such as ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole, has consistently increased. The only antibiotics that retained clinical utility were azithromycin and carbapenems.

S. Paratyphi A: Displayed stability in resistance trends, remaining largely susceptible to traditional first-line agents and cephalosporins. However, the consistent universal resistance to ciprofloxacin suggests that fluoroquinolones are no longer viable for the treatment of paratyphoid fever. These findings underscore the emergence and sustained circulation of XDR S. Typhi in KPK, with S. Paratyphi A showing a different resistance trajectory. The results align with previously reported national surveillance data, reinforcing the urgent need for antimicrobial stewardship and vaccination strategies.[5,9]

This study demonstrates the alarming escalation of AMA in S. Typhi isolates from KPK, consistent with trends reported in other provinces of Pakistan.[5.9] The most striking finding is the 100% resistance to fluoroquinolones, effectively rendering this class obsolete for therapeutic use. Cephalosporin resistance rates exceeding 90% highlight the widespread dominance of XDR. The reported cephalosporin resistance rates exceeding 90% conform with the definition of extensively drug-resistant (XDR) Salmonella typhi strains, since XDR S. typhi is defined as resistance to first-line agents, fluoroquinolones, and third-generation cephalosporins. Typhi strains in this region.[3,5] These results confirm that Pakistan remains a global epicenter for XDR typhoid with serious implications for treatment outcomes and public health security. Our findings also align with global evidence that azithromycin and carbapenems remain the only reliable therapeutic options for typhoid management.[10,11] However, the emergence of azithromycin

resistance, though rare in our dataset (0.2%), has been increasingly reported in South Asia, signaling the potential erosion of the last effective oral therapy.[12] This situation underscores the fragility of the therapeutic arsenal against typhoid fever, leaving carbapenems as the final line of defense, a class of drugs that should be preserved for life-threatening infections only. S. Paratyphi A showed a markedly different resistance profile compared to S. Typhi. While it exhibited universal fluoroquinolone resistance, it remained fully susceptible to first-line antibiotics and cephalosporins. While the isolates exhibited universal fluoroquinolone resistance, they remained fully susceptible to first-line antibiotics and cephalosporins. This pattern suggests that selective antibiotic pressure is a significant factor influencing the development of resistance in S. typhi. This suggests that antibiotic pressure has significant resistance in S. Typhi, possibly because of differences in transmission dynamics, infection burden, and exposure to antimicrobial therapies. Nonetheless, the presence of complete fluoroquinolone resistance in S. Paratyphi A is concerning and reflects the long-standing misuse and over-prescription of this antibiotic class in Pakistan.[13]

Public health implications: The findings of this study have many urgent implications for public health practice and policy.

Antimicrobial stewardship: There is an urgent need for strict antimicrobial stewardship programs at both hospital and community levels. This includes regulating over-the-counter sales, establishing standardized prescribing guidelines, and providing physician training to reduce irrational antibiotic use ^[13]. Without these measures, selective pressure will continue to accelerate the development of resistance.

Vaccination: Preventive strategies, particularly the scaling up of typhoid conjugate vaccine (TCV) campaigns, remain the most effective long-term solution. Widespread immunization can reduce disease incidence, limit transmission of resistant strains, and protect vulnerable populations in endemic regions.[1,8]

Surveillance: Sustained genomic and phenotypic surveillance of S. Typhi and S. Paratyphi A is crucial for detecting early signs of emerging resistance, particularly against azithromycin.[12,14] Surveillance data should be integrated into national policy frameworks to guide empirical therapy and inform vaccine deployment strategies.

Global health perspective: Since international travel has been linked to the exportation of XDR typhoid cases, including those originating from Pakistan, the threat extends beyond national boundaries.[3,10] Addressing this issue is therefore not only a domestic priority but also a global health security concern requiring international collaboration in containment and monitoring.

XDR typhoid has emerged as a critical public health threat in Pakistan, with resistance to fluoroquinolones and third-generation cephalosporins now firmly established.[3,5,9] The current findings from Khyber Pakhtunkhwa mirror national reports and highlight that S. Typhi is approaching pan-resistance, with only azithromycin and carbapenems retaining clinical efficacy.[10,11] This reliance on a limited therapeutic arsenal is precarious, particularly given growing concerns over emerging azithromycin resistance in South Asia.[12] To avert the escalation of a pan-drug-resistant epidemic, urgent, multi-pronged interventions are required. Strengthening antimicrobial stewardship at the hospital and community levels is imperative to curb irrational prescribing and safeguard the last remaining options.[13] Parallel to this, the expansion of TCV programs must be prioritized to reduce disease incidence and transmission of resistant strains.[1,8] Finally, continuous surveillance, both genomic and phenotypic, is essential to detect early shifts in resistance patterns and inform treatment guidelines and vaccine policy.[12,14,15] Taken together, these findings reinforce that Pakistan stands at a decisive turning point in the fight against typhoid. Without immediate action, the potential of pan-resistant Salmonella strains may soon become a reality with devastating consequences for clinical care and international health security.

Not reported

The authors affirm that this research was entirely self-financed, with no external funding, institutional grants, or sponsorship received. All costs associated with study design, data collection, analysis, and manuscript preparation were borne solely by the authors.

Corresponding Author:
Bilal Noor
Department of Pediatrics and Neonatology
THQ Hospital Central Kurram Dogar, Pakistan,
Email: Bilalzk261@gmail.com

Co-Authors:
Kashif Ullah
Medical Officer and in Charge Nursery
Nasir Ullah Babar Memorial Hospital, Peshawar, Pakistan

Muhammad Suliman
Department of Pathology
THQ Hospital Central Kurram Dogar Medical Lab Technologist, Kurram, Pakistan

Hamid Iqbal, Rehman Gul, Khadija Aziz
Department of Pediatric Medicine
Nasir Ullah Babar Memorial Hospital, Peshawar, Pakistan

Ziadullah Shah
Department of Pediatric and Neonatology
Nasir Ullah Babar Memorial Hospital, Peshawar, Pakistan

Dr. Bilal Noor served as the principal investigator and main corresponding author, supervising the study design, data interpretation, and manuscript preparation. Dr. Kashif Ullah contributed to data collection and assisted as a co-correspondent. Muhammad Suliman was responsible for data collection, review, and laboratory reporting. Dr. Hamid Iqbal assisted with reference management, manuscript design, and overall review of the article. Dr. Khadija Aziz contributed to reference management and assisted in the review process. Dr. Ziadullah Shah’s contribution is to be provided.

Ethical approval for this study was obtained from the institutional review board (IRB) of THQ Hospital, Dogar, Central Kurram (Ref No. 1325) prior to initiation of data collection.

The Authors declare no conflict of interest.

None

https://doi.org/10.63096/medtigo3062341