Typhoidal Salmonella strains in Pakistan: an impending threat of extensively drug-resistant Salmonella Typhi

Prevalence of the Antibiotic Resistance of Salmonella typhi and Salmonella paratyphi in Pakistan: A Systematic Review and Meta-analysis

Background

Antibiotic resistance to Salmonella is a significant threat to public health globally, particularly in low- and middle-income countries such as Pakistan. This study reviews the existing literature to determine the pooled prevalence of antibiotic resistance among Salmonella typhi and Salmonella paratyphi strains across Pakistan in the past decade, including the emergence of extended-spectrum β-lactamase.

Methods

Six databases were searched for studies published from January 2014 to December 2024. Studies were screened for relevance, and data were extracted on antibiotic susceptibility among human S typhi and S paratyphi isolates. Their quality was assessed per the Joanna Briggs Institute checklist. A random effects model was employed by R statistical software (version 4.4) to calculate the pooled resistance rates.

Results

Thirty-one studies met the inclusion criteria after full-text screening. The analysis revealed significant resistance rates to commonly used antibiotics for S typhi, including nalidixic acid (92%; 95% CI, 88%-95%), ampicillin (80%; 95% CI, 66%-89%), ciprofloxacin (64%; 95% CI, 48%-77%), azithromycin (7%; 95% CI, 3%-16%), and meropenem (2%; 95% CI, 1%-3%), with notable variations across cities, and for S paratyphi, such as nalidixic acid (91%; 95% CI, 82%-96%), ampicillin (34%; 95% CI, 21%-50%), ciprofloxacin (51%; 95% CI, 25%-77%), azithromycin (4%; 95% CI, 1%-12%), and meropenem (2%; 95% CI, 1%-5%). In S typhi, 29% and 25% of patients had multidrug resistance (95% CI, 21%-41%) and extensive drug resistance (95% CI, 12%-44%), respectively; corresponding rates for S paratyphi were 9% (95% CI, 2%-28%) and 2% (95% CI, 1%-7%).

Conclusions

The findings revealed the alarming prevalence of antibiotic-resistant Salmonella in Pakistan and the need for updated treatment guidelines. Public health strategies must focus on improving antibiotic use and developing alternative treatment options to mitigate the rising threat of resistant Salmonella strains. Continued research, policy intervention, and national and international cooperation are essential to safeguard public health and ensure effective management of enteric fever.

Antibiotic resistance in the Middle East and Southern Asia: a systematic review and meta-analysis

Introduction

Despite global surveillance efforts, antibiotic resistance (ABR) is difficult to address in low- and middle-income countries (LMICs). In the absence of country-wide ABR surveillance data, peer-reviewed literature is the next most significant source of publicly available ABR data. Médecins Sans Frontières conducted this review in hopes of using the pooled findings to inform treatment choices in the studied countries where sufficient local ABR data are unavailable.

Methods

A systematic literature review reporting ABR rates for six infection sites in nine countries in the Middle East and Southern Asia was conducted. PubMed was used to identify literature published between January 2012 and August 2022. A meta-analysis of the included studies (n = 694) was conducted, of which 224 are reviewed in this paper. The JBI critical appraisal tool was used to evaluate risk of bias for included studies.

Results

This paper focuses on sepsis, burns and wound infections, specifically, with the largest number of papers describing data from Iran, Türkiye and Pakistan. High (>30%) resistance to recommended first-line antibiotics was found. Gram-negative resistance to ceftriaxone, aminoglycosides and carbapenems was high in burn-related infections; colistin resistance among Klebsiella pneumoniae isolates in Pakistan was alarmingly high (81%).

Conclusions

High-quality data on ABR in LMIC settings remain difficult to obtain. While peer-reviewed literature is a source of publicly available ABR data, it is of inconsistent quality; the field also lacks agreed reporting standards, limiting the capacity to pool findings. Nonetheless, high resistance to first-line antibiotics underscores the need for improved localized surveillance and stewardship.

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.

Phage-antibiotic synergism against Salmonella typhi isolated from stool samples of typhoid patients

BACKGROUND

Typhoid fever is a fatal disease in humans that is caused by Salmonella typhi. S. typhi infections need immediate antibiotic therapy, and their extensive use has led to multidrug-resistant (MDR) pathogens. The use of bacteriophages is becoming a new way to treat these resistant bacteria. This research was directed to bacteriophage isolation against S. typhi and to determine phage-antibiotic synergism.

AIMS

To isolate bacteriophages targeting S. typhi, the causative agent of typhoid fever, and investigate their potential synergistic effects when combined with antibiotics.

STUDY DESIGN

A cross-sectional study.

METHODS

The Widal test was positive; twenty diarrheal stool samples were taken, and for confirmation of S. typhi, different biochemical tests were performed. The disc-diffusion technique was used to determine antimicrobial resistance, and the double agar overlay method was used for bacteriophage isolation from sewage water against S. typhi. To test antibiotic-phage synergism, the S. typhi bacteria was treated by phages together with varying antibiotic concentrations.

RESULTS

Eleven samples were positive for S. typhi with black colonies on SS-agar. These were catalase and MR positive with alkali butt on TSI. Clear plaques were observed after the agar overlay. Isolated phages were stable at various pH and temperature levels. Synergism was observed on agar plate. The zone was enlarged when phages were combined with bacterial lawn culture and ciprofloxacin disk. Bacterial growth inhibition had a significant p-value of 0.03 in titration plates, with the phage-ciprofloxacin combination being more effective than the phage and antibiotic alone.

CONCLUSION

The study highlights the synergistic effects of isolated bacteriophages with antibiotics, which are not only effective against S. typhi infection but also decrease antibiotic resistance.

Use of Biomaterials in 3D Printing as a Solution to Microbial Infections in Arthroplasty and Osseous Reconstruction

The incidence of microbial infections in orthopedic prosthetic surgeries is a perennial problem that increases morbidity and mortality, representing one of the major complications of such medical interventions. The emergence of novel technologies, especially 3D printing, represents a promising avenue of development for reducing the risk of such eventualities. There are already a host of biomaterials, suitable for 3D printing, that are being tested for antimicrobial properties when they are coated with bioactive compounds, such as antibiotics, or combined with hydrogels with antimicrobial and antioxidant properties, such as chitosan and metal nanoparticles, among others. The materials discussed in the context of this paper comprise beta-tricalcium phosphate (β-TCP), biphasic calcium phosphate (BCP), hydroxyapatite, lithium disilicate glass, polyetheretherketone (PEEK), poly(propylene fumarate) (PPF), poly(trimethylene carbonate) (PTMC), and zirconia. While the recent research results are promising, further development is required to address the increasing antibiotic resistance exhibited by several common pathogens, the potential for fungal infections, and the potential toxicity of some metal nanoparticles. Other solutions, like the incorporation of phytochemicals, should also be explored. Incorporating artificial intelligence (AI) in the development of certain orthopedic implants and the potential use of AI against bacterial infections might represent viable solutions to these problems. Finally, there are some legal considerations associated with the use of biomaterials and the widespread use of 3D printing, which must be taken into account.

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.

Antimicrobial Properties of Capsaicin: Available Data and Future Research Perspectives

Capsaicin is a phytochemical derived from plants of the genus Capsicum and subject of intensive phytochemical research due to its numerous physiological and therapeutical effects, including its important antimicrobial properties. Depending on the concentration and the strain of the bacterium, capsaicin can exert either bacteriostatic or even bactericidal effects against a wide range of both Gram-positive and Gram-negative bacteria, while in certain cases it can reduce their pathogenicity by a variety of mechanisms such as mitigating the release of toxins or inhibiting biofilm formation. Likewise, capsaicin has been shown to be effective against fungal pathogens, particularly Candida spp., where it once again interferes with biofilm formation. The parasites Toxoplasma gondi and Trypanosoma cruzi have been found to be susceptible to the action of this compound too while there are also viruses whose invasiveness is significantly dampened by it. Among the most encouraging findings are the prospects for future development, especially using new formulations and drug delivery mechanisms. Finally, the influence of capsaicin in somatostatin and substance P secretion and action, offers an interesting array of possibilities given that these physiologically secreted compounds modulate inflammation and immune response to a significant extent.

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

Background

The emergence of extensively drug-resistant (XDR) typhoid in Pakistan has endangered the treatment options available to manage this infection. Third generation cephalosporin were the empiric choice to treat typhoid fever in Pakistan, but acquisition of ESBLs have knocked them out of the arsenal. The current empiric choice is azithromycin which is vulnerable to resistance too. This study aimed to assess the burden of XDR typhoid and the frequency of resistance determinants in blood culture samples collected from different hospitals in Lahore, Pakistan.

Methods

A total of 835 blood cultures were collected from different tertiary care hospitals in Lahore during January 2019 to December 2021. Among 835 blood cultures, 389 Salmonella Typhi were identified, and 150 were XDR S. Typhi (resistant to all recommended antibiotics). Antibiotics resistance genes of the first-line drugs (bla_TEM-1, catA1, sul1, and dhfR7) and second line drugs (gyrB, gyrA, qnrS, ParC and ParE) were investigated among XDR S. Typhi. There were different CTX-M genes isolated using the specific primers, bla_CTX-M-U, bla_CTX-M-1, bla_CTX-M-15, bla_CTX-M-2, bla_CTX-M-8 and bla_CTX-M-9.

Results

Antibiotic resistant genes of the first-line drugs were isolated with different frequency, bla_TEM-1 (72.6%), catA1 (86.6%), sul1 (70%), and dhfR7 (56%). Antibiotics resistance genes of second-line drugs were isolated as: gyrB (60%), gyrA (49.3%), qnrS (32.6%), parC (44%) and parE (28%). Among CTX-M genes, bla_CTX-M-U (63.3%) was the most frequent followed by bla_CTX-M-15 (39.3%) and bla_CTX-M-1 (26%).

Conclusion

Our study concluded that XDR isolates circulating in Pakistan have acquired first-line and second-line antibiotic resistant genes quite successfully along with CTX-M genes (ESBLs) rendering them resistant to the third generation cephalosporins as well. Emergence of azithromycin resistance in XDR S. Typhi which is currently used as an empiric treatment option is worrisome and needs to be monitored carefully in endemic countries like Pakistan.

Clinical Characteristics and Antibiotics Sensitivity of Culture Positive Typhoid Fever Patients in Baghdad Teaching Hospital - A Single Center Study

BACKGROUND: Enteric fever caused by Salmonella Typhi is an endemic disease in Iraq. Variations in presentations make it a diagnostic challenge. If untreated or treated inappropriately then it is a serious disease with potentially life-threatening complications. The recent emergence of drug resistant strains of S. Typhi is a rising public health problem and a clinical concern to the physician. AIM: The objectives of the study were to assess and describe the patterns of antimicrobial resistance, clinical characteristics, epidemiological distribution, and complications of typhoid fever. PATIENTS AND METHODS: Fifty cases of typhoid fever (culture proven) were collected during the period from February 2019 to November 2019 in the medical wards of Baghdad Teaching Hospital. Detailed history, physical examination, and laboratory investigations were conducted and statistical analysis of the results was done, prospective observational study was conducted. RESULTS: During the study period, 50 cases of typhoid fever were documented, mean age of presentation was 30.7 ± 12.8, 60% of the cases were male gender, gastrointestinal complications were the most common (90%) followed by hematological complications (71%). Mortality of typhoid fever in our study was 2%. High percentage of resistance to third generation cephalosporins, ciprofloxacin, and azithromycin was found (96%, 56%, and 56%, respectively) while good sensitivity to trimethoprim and meropenem was found (94% and 76%, respectively). Significant association was also found between the development of typhoid fever complications and the presence of anemia, thrombocytopenia, lymphopenia, and eosinopenia. Significant association was also found between the complications and the infection with strains resistant to cephalosporins, ciprofloxacin, and azithromycin. CONCLUSIONS: There is a concerning increase in resistance toward cephalosporins, ciprofloxacin, and azithromycin while meropenem and trimethoprim are emerging as effective drugs. There was high incidence of complications found (84%).Lymphopenia, anemia, eosinopenia, and thrombocytopenia are independent risk factors for the development of complications of typhoid fever.

Capsaicin Potently Blocks Salmonella typhimurium Invasion of Vero Cells

Salmonella typhimurium (S. typhimurium) is one of the major food and waterborne bacteria that causes several health outbreaks in the world. Although there are few antibiotics against this bacterium, some of these drugs are challenged with resistance and toxicity. To mitigate this challenge, our group explored the ethnomedicinal/herbalism knowledge about a certain spice used in Northern Ghana in West Africa against bacterial and viral infection. This plant is Capsicum chinense (C. chinense). The plant is one of the commonest food spices consumed across the world. The seed of the plant contains both capsaicin and dihydrocapsaicin. Apart from capsaicin and dihydrocapsaicin, other major capsaicinoids in C. chinense include nordihydrocapsaicin, homodihydrocapsaicin, and homocapsaicin. In this pilot work, we investigated the antibacterial activity of pure capsaicin and capsaicin extract obtained from C. chinense against S. typhimurium in vitro. Capsaicin extract showed potent inhibition of S. typhimurium growth at concentrations as low as 100 ng/mL, whereas pure capsaicin comparatively showed poorer inhibition of bacteria growth at such a concentration. Interestingly, both capsaicin extract and pure capsaicin were found to potently block a S. typhimurium invasion of the Vero cell in vitro. Taken together, we believed that capsaicin might work synergistically with dihydrocapsaicin or the other capsaicinoids to inhibit S. typhimurium growth, whereas individually, capsaicin or dihydrocapsaicin could potently block the bacteria entry and invasion of Vero cells.

Assessment of without prescription antibiotic dispensing at community pharmacies in Hazara Division, Pakistan: A simulated client's study

Antibiotics dispensing without a prescription is an irrational practice and can increase the risk of antibiotic resistance, which is a significant public health concern around the globe. This study was aimed to determine the extent to which antibiotics are supplied without prescription in the community pharmacies (CPs) at Hazara Division from November 2020 to February 2021. The simulated client method (SCM) was used, and the data were gathered, recorded, and analyzed through different statistical methods with descriptive and inferential techniques. The antibiotic dispensing was observed in CPs (90.5%), the most dispensed antibiotics were azithromycin (29.4%) and ciprofloxacin (46.5%) respectively. Furthermore, visited medical stores/ drug outlets, 9.5% of the visited stores denied dispensing of antibiotics because they preferred a referral to visit physicians (23. 9%) and (12.8%) did not had the antibiotics at the time of visits. Antibiotics were more obtainable in retail medical stores (AOR = 8.6, 95 percent Cl: 3.0–24.7; p = 0.001) than in pharmacies. In rural areas antibiotics dispensing was more (p = 0.004) as compared to urban areas. Staff members also had asked about patient’s (17.7%) symptoms and drug allergies (12.3% and 3.9%), and (1.5%) they consoled them about their medications. The findings of this study indicate that nonprescription antibiotic sales are very common, despite national rules prohibiting this activity. When the simulated Client requested for any medication to relieve his or her discomfort, many antibiotics were given out without a prescription. Pharmacies/medical stores in Hazara Division selling antibiotics without a prescription are worrying and need immediate action by regulators.

An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58

Salmonella typhi is notorious for causing enteric fever which is also known as typhoid fever. It emerged as an extreme drug resistant strain that requires urgent attention to prevent its global spread. Statistically, about 11-17 million typhoid illnesses are reported worldwide annually. The only alternative approach for the control of this illness is proper vaccination. However, available typhoid vaccine has certain limitations such as poor long-term efficacy, and non-recommendation for below 6 years children, which opens the avenues for designing new vaccines to overcome such limitations. Computational-based reverse vaccinology along with subtractive genomics analysis is one of the robust approaches used for the prioritization of vaccine candidates through direct screening of genome sequence assemblies. In the current study, we have successfully designed a peptide-based novel antigen chimeric vaccine candidate against the XDR strain of S. typhi H58. The pipeline revealed four peptides from WP_001176621.1 i.e., peptidoglycan-associated lipoprotein Pal and two peptides from WP_000747548.1 i.e., OmpA family lipoprotein as promising target for the induction of immune response against S. typhi. The six epitopes from both proteins were found as immunogenic, antigenic, virulent, highly conserved, nontoxic, and non-allergenic among whole Salmonella H58 proteome. Furthermore, the binding interaction between a chimeric vaccine and human population alleles was unveiled through structure-based studies. So far, these proteins have never been characterized as vaccine targets against S. typhi. The current study proposed that construct V2 could be a significant vaccine candidate against S. typhi H58. However, to ascertain this, future experimental holistic studies are recommended as follow-up.

Prevalence and antimicrobial susceptibility level of typhoid fever in Ethiopia: A systematic review and meta-analysis

Typhoid fever continues to be a health challenge in low-and middle-income countries where access to clean water and sanitation infrastructure is scarce. The non-confirmatory diagnostic method continues to hinder effective diagnosis and treatment, ensuring in a high antimicrobial resistance. This systematic review and meta-analysis aimed to estimate the pooled prevalence and antimicrobial susceptibility level of typhoid fever in Ethiopia. The review was designed based on the condition-context-population review approach. Fifteen eligible articles were identified from PubMed, Google Scholar, and Science Direct databases. Risk of bias and quality of studies were assessed using the Joanna Briggs Institute's appraisal criteria. Heterogeneity was assessed using Cochran's Q test and I2 statistics. The review protocol was registered in PROSPERO (registration number CRD42021224478). The estimated pooled prevalence of typhoid fever from blood and stool culture diagnosis was 3% (95% CI: 2%-4%, p < 0.01) (I2  = 82.25) and Widal test examination 33% (95% CI: 22%-44%) (I2  = 99.14). The sub-group analyses identified a lower detection of typhoid fever of 2% (95% CI: 1%-3%) among febrile patients compared to typhoid suspected cases of 6% (95% CI: 2%-9%). The stool culture test identified was twofold higher, value of 4% (95% CI: 2%-7%) salmonella S. Typhi infection than blood culture test of 2% (95% CI: 1%-4%). The antimicrobial susceptibility of salmonella S. Typhi for antibiotics was 94%, 80% and 65% for ceftriaxone, ciprofloxacin, and gentamycin respectively. Low susceptibility of salmonella S. Typhi isolates against nalidixic acid 22% (95% CI: 2%-46%) and chloramphenicol 11% (95% CI: 2%-20%) were observed. The diagnosis of typhoid fever was under or overestimated depending on the diagnostic modality. The Widal test which identified as nonreliable has long been used in Ethiopia for the diagnosis of salmonella S. Typhi causing high diagnosis uncertainties. Antimicrobial susceptibility of salmonella S. Typhi was low for most nationally recommended antibiotics. Ethiopian Food and Drug Authority must strengthen its continued monitoring and enhanced national antimicrobial surveillance system using the best available state-of-the-art technology and or tools to inform the rising resistance of salmonella S. Typhi towards the prescription of standard antibiotics. Finally, it is crucial to develop an evidence-based clinical decision-making support system for the diagnosis, empiric treatment and prevention of antimicrobial resistance.

British Infection Association Guidelines for the Diagnosis and Management of Enteric Fever in England

Enteric fever (EF) is an infection caused by the bacteria called Salmonella Typhi or Paratyphi. Infection is acquired through swallowing contaminated food or water. Most EF in England occurs in people returning from South Asia and other places where EF is common; catching EF in England is rare. The main symptom is fever, but stomach pain, diarrhoea, muscle aches, rash and other symptoms may occur. EF is diagnosed by culturing the bacteria from blood and/or stool in a microbiology laboratory. EF usually responds well to antibiotic treatment. Depending on how unwell the individual is, antibiotics may be administered by mouth or by injection. Over the past several years, there has been an overall increase in resistance to antibiotics used to treat enteric fever, in all endemic areas. Additionally, since 2016, there has been an ongoing outbreak of drug-resistant EF in Pakistan. This infection is called extensively drug-resistant, or XDR, EF and only responds to a limited number of antibiotics. Occasionally individuals develop complications of EF including confusion, bleeding, a hole in the gut or an infection of the bones or elsewhere. Some people may continue to carry the bacteria in their stool for a longtime following treatment for the initial illness. These people may need treatment with a longer course of antibiotics to eradicate infection. Travellers can reduce their risk of acquiring EF by following safe food and water practices and by receiving the vaccine at least a few weeks before travel. These guidelines aim to help doctors do the correct tests and treat patients for enteric fever in England but may also be useful to doctors and public health professionals in other similar countries.

Disc Diffusion Testing of Azithromycin Against Clinical Isolates of Typhoidal Salmonellae: A Diagnostic Conundrum

Introduction: Typhoid remains a major healthcare problem in low and middle-income countries. The emergence of extremely drug-resistant (XDR) typhoid strains from the Indian subcontinent has led to very limited therapeutic options. Azithromycin being the only oral option for XDR typhoid faces a threat of rapid resistance due to its overuse after the COVID-19 pandemic.

Objective: To evaluate the reliability of azithromycin disc diffusion testing against clinical isolates of typhoidal salmonellae in comparison with E-test minimum inhibitory concentrations (MICs).

Study design: This is a cross-sectional validation study.

Place and duration of the study: The Department of Microbiology, Pakistan Navy Ship Shifa hospital, Karachi from June 1 to December 31, 2020.

Methodology: Antimicrobial susceptibility was performed by Kirby Bauer disc diffusion method for 60 isolates including Salmonella enterica ser. Typhi and Paratyphi A using Clinical Laboratory Standard Institute (CLSI) guidelines. MICs by the E-test method were determined for Azithromycin only.

Results: A significant proportion of the isolates (55%) had high azithromycin MIC in the wild-type distribution range (8-16 µg/ml). Ten (16.6%) isolates showed false resistance, i.e., zone diameter <13 mm by disc diffusion method when compared to E-test MIC results. Isolates with MICs close to breakpoint, i.e., 16 µg/ml were more likely to show discordant results. The sensitivity, specificity, negative predictive value, positive predictive value, and diagnostic accuracy of the disc diffusion method versus E-test were 100%, 83%, 100%, 9%, and 83%, respectively.

Conclusions: Disc diffusion method as recommended by CLSI is not reliable for azithromycin susceptibility testing particularly for isolates with high MICs in the susceptible range. The E-test method may be a better alternative to disc diffusion provided appropriate training is done prior to its application.

Progress on the national action plan of Pakistan on antimicrobial resistance (AMR): a narrative review and the implications

Introduction: The emergence of antimicrobial resistance (AMR) is a threat to public health. In 2015, the World Health Organization (WHO) introduced a global action plan to tackle AMR in the World Health Assembly. Pakistan's national action plan (NAP) for AMR was released in May 2017 by the Ministry of National Health Services. Based on the NAP, strategies have been initiated on a national and provincial scale in Pakistan.Areas covered: This narrative review of the five components of the Pakistan NAP has been undertaken to discuss some of the challenges in implementation of the NAP for AMR in Pakistan including different opinions and views of key stakeholders, combined with suggestions on potential ways to reduce the burden of the AMR.Expert opinion: Going forward, healthcare authorities should focus on screening and monitoring of all the objectives of the NAP by establishing proper policies as well as promoting antimicrobial stewardship interventions and Infection prevention and control (IPC) practices. Overall, the comprehensive strengthening of the healthcare system is required to adequately implement the NAP, tackle continued inappropriate antimicrobial use and high AMR rates in Pakistan.

Drug resistance in Salmonella Typhi: implications for South Asia and travel

PURPOSE OF REVIEW

Recent attempts at mapping Typhoid epidemiology have revealed an enormous burden of disease in developing countries. Countries hitherto believed to have a low incidence, such as the African subcontinent, on accurate mapping were found to have a significant burden of disease. Drug resistance, because of rampant overuse of antibiotics, has driven selection pressure to extensively drug-resistant typhoid becoming a reality in the Indian subcontinent. With widespread travel, importation of this variety of typhoid to nonendemic countries is likely to lead to outbreaks in a nonimmune population.

RECENT FINDINGS

A strain of extensively drug-resistant Salmonella Typhi isolated in Pakistan in 2016 has been responsible for multiple outbreaks in Pakistan and multiple travel-related cases all over the world in United States, UK, and Australia. This novel strain belongs to H58 lineage harbouring a plasmid encoding additional resistance elements like blaCTX-M-15 and a qnrS fluoroquinolone resistance gene. This resistance pattern has rendered many therapeutic options like Ceftriaxone and Fluoroquinolones clinically inactive impacting care in endemic and traveller populations alike.

SUMMARY

Changing epidemiology and drug resistance in typhoid indicates that it may be prudent to vaccinate nonimmune travellers travelling to typhoid endemic areas, especially the Indian subcontinent.

Antibiotyping and genotyping of extensively drug-resistant (XDR) Salmonella sp. isolated from clinical samples of Lahore, Pakistan

AIMS

Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi. The objective of this study was to evaluate the prevalence of XDR Salmonella among local population of Lahore and genotyping of isolates for antibiotic-resistant genes.

METHODS AND RESULTS

A total of 200 blood samples from suspected typhoid fever patients were collected. One hundred and fifty-seven bacterial samples were confirmed as Salmonella Typhi and 23 samples were confirmed as Salmonella Paratyphi after biochemical, serological and PCR based molecular characterization. Antibiogram analysis classified 121 (67·2%) Salmonella isolates as MDR and 62 isolates (34·4%) as XDR. The predominant resistance gene was ampC with 47·7% prevalence, followed by gyrA, catA1, tet(A), aac (3)-la, qnrS, bla_NDM-1 and bla_CTX-M-15 genes in 45·5, 40, 21·6, 18·3, 11·6, 2·2 and 0·5% isolates respectively. Sequence analysis showed the presence of sul1 and dfrA7 gene cassette arrays in 12 class 1 integron integrase positive isolates.

CONCLUSION

Large number of clinical XDR S. Typhi-resistant against third generation cephalosporins have been reported.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current study highlights the possible emergence of clinical XDR S. Typhi cases in Lahore, Pakistan. Potential attribution of phenotypic and genotypic XDR cases may help to contribute targeted therapy.

Antibiotic resistance in Pakistan: a systematic review of past decade

Background

During the last six decades, extensive use of antibiotics has selected resistant strains, increasing the rate of fatal infectious diseases, and exerting an economic burden on society. This situation is widely accepted as a global problem, yet its degree is not well elucidated in many regions of the world. Up till now, no systemic analysis of Antimicrobial resistance (AMR) in Pakistan has been published. The current study aims to describe the antibiotic-resistance scenario of Pakistan from human samples of the last 10 y, to find the gaps in surveillances and methodology and recommendations for researchers and prescribers founded on these outcomes.

Methods

Original research articles analyzed the pattern of Antibiotic resistance of any World Health Organization (WHO) enlisted priority pathogens in Pakistan (published onward 2009 till March 2020), were collected from PubMed, Google scholar, and PakMedi Net search engines. These articles were selected based on predefined inclusion and exclusion criteria. Data about the study characteristics and antibiotic-resistance for a given bacterium were excluded from literature. Antibiotic resistance to a particular bacterium was calculated as a median resistance with 95% Confidence Interval (CI).

Results

Studies published in the last 10 y showed that Urinary Tract Infection (UTI) is the most reported clinical diagnosis (16.1%) in Pakistan. E. coli were reported in 28 (30.11%) studies showing high resistance to antibiotics’ first line. Methicillin-resistant Staphylococcus aureus (MRSA) was found in 49% of S. aureus’ total reported cases. Phenotypic resistance pattern has mostly been evaluated by Disk Diffusion Method (DDM) (82.8%), taken Clinical Laboratory Standards Institute (CLSI) as a breakpoint reference guideline (in 79.6% studies). Only 28 (30.11%) studies have made molecular identification of the resistance gene. blaTEM (78.94% in Shigella spp) and blaNDM-1 (32.75% in Klebsiella spp) are the prominent reported resistant genes followed by VanA (45.53% in Enterococcus spp), mcr-1 (1.61% in Acinetobacter spp), and blaKPC-2 (31.67% in E. coli). Most of the studies were from Sindh (40.86%), followed by Punjab (35.48%), while Baluchistan’s AMR data was not available.

Conclusion

Outcomes of our study emphasize that most of the pathogens show high resistance to commonly used antibiotics; also, we find gaps in surveillances and breaches in methodological data. Based on these findings, we recommend the regularization of surveillance practice and precise actions to combat the region’s AMR.

Trends of Antimicrobial Resistance in Typhoidal Strains of Salmonella in a Tertiary Care Hospital in Pakistan

INTRODUCTION

Enteric fever or typhoid fever is a major public health issue affecting greater than 27 million individuals globally and is responsible for greater than 200,000 deaths per year. Due to the extensive overuse of antimicrobials, the world is moving toward a pre-antibiotic era. The emergence and transmission of antibiotic-resistant Salmonella species are a global threat and a serious concern in developing countries such as Pakistan. This study aimed to determine the trends in antimicrobial resistance (AMR) of typhoidal strains of Salmonella in a tertiary care hospital in Pakistan.

MATERIALS AND METHODS

It was a descriptive, cross-sectional study conducted in the pathology department of Sharif City Hospital, Lahore, after approval by the ethical committee of the institution. A total of 50 blood culture specimens positive for Salmonella typhi and Salmonella paratyphi from January 2019 to March 2020 were included by the non-probability consecutive sampling technique. The samples were processed by conventional bacteriological methods for isolation and identification. The antimicrobial susceptibility testing was done by the Kirby-Bauer disc diffusion method as recommended by the Clinical and Laboratory Standard Institute (CLSI). The statistical package for social sciences (SPSS, IBM Corp., Armonk, NY) version 25 was used for data entry and analysis.

RESULTS

Among the first-line drugs (ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole), 70% of strains were resistant, and only 30% strains were sensitive to them. Among the cephalosporins, 52% strains were sensitive to ceftriaxone, and 48% strains were sensitive to ceftazidime, cefotaxime, and cefepime. Twenty-four percent of strains were sensitive to ciprofloxacin. Only 50% of strains were sensitive to ampicillin-sulbactam, and 92% of strains were sensitive to piperacillin-tazobactam. All the strains were 100% sensitive to imipenem and meropenem; 96% of strains were sensitive to co-amoxiclav, doxycycline, and azithromycin. The frequency of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Salmonella species was 16% and 54%.

CONCLUSION

The increasing frequency of MDR and XDR Salmonella species in Pakistan is a major concern. A significant percentage of the typhoidal strains of Salmonella is resistant to the first-line (16%) and second-line (54%) antibiotics. Carbapenems and azithromycin are the last resort of therapy in such cases.

Case Report: Ceftriaxone-Resistant Invasive Salmonella Enteritidis Infection with Secondary Hemophagocytic Lymphohistiocytosis: A Contrast with Enteric Fever

In contrast to enteric fever, reports of secondary hemophagocytic lymphohistiocytosis (HLH) in invasive non-typhoidal salmonellosis are scarce. We report a child with ceftriaxone-resistant invasive Salmonella Enteritidis infection with secondary HLH, who was successfully managed with intravenous meropenem. Secondary HLH in the context of S. Enteritidis has not been described before.

Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan

Extensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterization of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan. Isolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby–Bauer method. These findings were confirmed using Illumina whole genome nucleotide sequence data. All sequences were compared to the outbreak strain from Southern Pakistan and typed using the S. Typhi genotyping scheme. All isolates were confirmed by a sequence analysis to harbor an IncY plasmid and the CTX-M-15 ceftriaxone resistance determinant. All isolates were of the same genotypic background as the outbreak strain from Sindh province. We report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing.

First Case of Typhoid Fever due to Extensively Drug-resistant Salmonella enterica serovar Typhi in Italy

Typhoid fever is a potentially severe and occasionally life-threatening bacteraemic illness caused by Salmonella enterica serovar Typhi (S. Typhi). In Pakistan, an outbreak of extensively drug-resistant (XDR) S. Typhi cases began in November 2016. We report on a five-year-old boy who contracted enteric fever while travelling in Pakistan and was diagnosed after returning to Italy in September 2019. Blood culture isolated Salmonella enterica serovar Typhi that was XDR to all first-line antibiotics, including ceftriaxone and fluoroquinolones. Empiric therapy was switched to meropenem, and the patient recovered completely. Whole-genome sequencing showed that this isolate was of haplotype H58. The XDR S. Typhi clone encoded a chromosomally located resistance region and harbored a plasmid encoding additional resistance elements, including the blaCTX-M-15 extended-spectrum β-lactamase and the qnrS fluoroquinolone resistance gene. This is the first case of typhoid fever due to XDR S. Typhi detected in Italy and one of the first paediatric cases reported outside Pakistan, highlighting the need to be vigilant for future cases. While new vaccines against typhoid are in development, clinicians should consider adapting their empiric approach for patients returning from regions at risk of XDR S. Typhi outbreak with typhoid symptoms.