Prevalence of Salmonella Typhi, its associated factors and antimicrobial susceptibility profile among patients attending Hawassa University Comprehensive Specialized Hospital, Hawassa, Ethiopia.

INTRODUCTION: Salmonella Typhi infections cause significant morbidity and mortality worldwide, especially in developing countries including Ethiopia. This study aimed to determine the prevalence of Salmonella Typhi, its associated factors and antibiotic susceptibility profile among suspected typhoid patients. METHODS: A cross-sectional study was conducted on 270 typhoid fever suspected patients at Hawassa University Comprehensive Specialized Hospital from June 2022 to September 2022. Data were collected using questionnaires by face-to-face interview. Stool samples for microbiological culture, blood samples for S. Typhi IgM/Entero-check WB rapid test and isolates for antimicrobial susceptibility tests were used through standard procedures and according to the reagents manufactures' instructions. Hygiene implementation of patients was also assessed using interview. Sociodemographic and clinical characteristics of the patient's were considered. Descriptive statistics were used to summarize the data, and logistic regression model analysis was performed to assess associations between S. Typhi infection and the associated sociodemographic and clinical factors. RESULTS: The prevalence of S. Typhi IgM/Entero-check WB rapid test and stool culture results were 3.3%; (95% CI: 1.5-5.6) and 3.7%; (95% CI: 1.9-6.3) respectively. Not washing hands after latrine [AOR = 0.85, 95% CI (0.15-4.79), p = 0.05] is not significant but, not washing hands before meal [AOR = 0.053, 95% CI (0.08-0.36), p = 0.03], eating raw vegetables [AOR = 0.024, 95% CI (0.001-0.48), p = 0.015] and drinking water from a stream [AOR = 0.12, 95% CI (0.19-0.70), p = 0.001] were significantly associated with S. Typhi infection, but in terms of AOR, all are preventive. Susceptibility of isolates was 9/10 (90%), 8/10 (80%), and 8/10 (80%) to ciprofloxacin, ceftriaxone, and chloramphenicol, respectively. The majorities 100% and 80% of the isolates were resistant to ampicillin and cotrimoxazole, respectively. About 40% of the isolates were MDR. CONCLUSION: The prevalence of Salmonella Typhi with MDR has been observed. Therefore, health programmers and stakeholders should make efforts to improve the habit of sanitation, strengthen the capacity of laboratory diagnostic methods and increase awareness of the misprescription and misuse of antibiotics to reduce the impact of MDR bacteria.

Multidrug-resistant Salmonella Typhi among symptomatic and asymptomatic children in informal settlements in Nairobi, Kenya.

BACKGROUND: The emergence and persistence of multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) infections is a significant global health problem. The carrier state of typhoid makes it prudent to conduct routine surveillance for both acute cases and carriers especially those caused by MDR S. Typhi. We report on the prevalence of MDR S. Typhi, resistance phenotypes and antimicrobial resistance genes detected in symptomatic and asymptomatic children living in informal settlements in Nairobi, Kenya. METHODS: 215 archived presumed S. Typhi isolates from stool samples provided by children ≤ 16 years collected from 2013 to 2018 were revived in May, 2022 and confirmed using culture and antisera serotyping. The Kirby Bauer disc diffusion technique was used to test the S. Typhi against 14 antibiotics. The MDR S. Typhi (resistant to ampicillin, chloramphenicol and sulfamethoxazole trimethoprim) which in addition were also resistant to either a cephalosporin or a fluoroquinolone were analyzed for Beta lactams and quinolone resistance genes using polymerase chain reaction. RESULTS: A total of 215 isolates were confirmed to be positively S. Typhi; of these, 105 (49%) and 110 (51%) were from symptomatic and asymptomatic children respectively. On average, S. Typhi resistance from asymptomatic and symptomatic children against 1st line drugs was observed at; 77% &70%, ampicillin; 60% & 64%, sulfamethoxazole-trimethoprim, and 45% & 54%, chloramphenicol respectively. Multi drug resistance was observed in 90 (42%) of the isolates, of these, 44 (49%) were isolated from symptomatic and 46 (51%) from asymptomatic children. Fifteen resistance phenotypes (p) were observed with, ampicillin/chloramphenicol/sulfamethoxazole-trimethoprim/nalidixic acid (amp/chl/sxt/na) as the most common among the symptomatic 43/90 (48%) and asymptomatic 55/90 (61%) children. The blaTEM-D, AMR genes were detected in 37/44 (84%) S. Typhi isolates, out of this 18 (49%) were from symptomatic while 19 (51%) were from asymptomatic children respectively. CONCLUSION: The carriage of MDR S. Typhi among the asymptomatic children is concerning as they can act as potential transmitters of the typhoid disease to unsuspecting children. These study findings highlight the need for continued surveillance of antimicrobial resistance and mass immunization of children living in these urban informal areas.

Infection of the ovarian cyst: a rare presentation of extraintestinal salmonellosis.

A woman in her early 20's presented with fever and unintentional weight loss of 4 kg over a period of 1 month and abdominal pain for 10 days. Empirical antibiotic therapy administered prior to hospitalisation was not successful. Evaluation for fever was unrewarding except for an abnormal ultrasound which showed two cysts with the largest dimension of 9 cm in the right adnexal region. All blood cultures were sterile. She underwent laparoscopic cystectomy. Bacterial culture of cyst fluid grew Salmonella enterica subspecies enterica serotype Typhi which was found to be resistant to fluoroquinolones. The case emphasises the fact that localised infection of the ovarian cyst can occur in extraintestinal salmonellosis that can have a negative blood culture and can mimic ovarian malignancy.

Environmental surveillance for Salmonella Typhi in rivers and wastewater from an informal sewage network in Blantyre, Malawi.

Environmental surveillance for Salmonella Typhi may provide information on the community-level dynamics of typhoid fever in resource poor regions experiencing high disease burden. Many knowledge gaps concerning the feasibility of ES remain, especially in areas lacking formal sewage systems. We implemented protocols for S. Typhi ES, including site selection and catchment population estimation, sample concentration and testing using qPCR for S. Typhi specific gene targets. Between May 2021 and May 2022, we collected grab samples and Moore swabs from 43 sites in Blantyre, Malawi. Catchment characteristics, water quality, and human faecal contamination (qPCR for Bacteroides HF183) were also recorded. Their association with S. Typhi detection was investigated using a logistic mixed-effects regression analysis. Prevalence of S. Typhi in ES samples was 2.1% (1.1-4.0%) and 3.9% (1.9-7.9%) for grab and Moore swab samples, respectively. HF183 was associated S. Typhi positivity, with a unit increase in log genome copies/microlitre increasing the odds of detection of S. Typhi by 1.56 (95% CI: 1.29-1.89) and 1.33 (1.10-1.61) in Moore swabs and grab samples, respectively. The location and timing of S. Typhi detection through ES was not associated with the incidence of typhoid fever reported in associated catchment populations. During this period of relatively low typhoid fever incidence, wastewater surveillance continued to detect S. Typhi in human sewage and wastewater suggesting that ES using natural river systems can be a sensitive indicator of transmission.

Molecular Detection of Salmonella typhi Isolated from Patients Undergoing Gallbladder Cholecystectomy in Baghdad.

BACKGROUND: Salmonella typhi is a specific strain of the Salmonella bacterium, responsible for triggering typhoid fever; a significant public health concern in developing nations. OBJECTIVE: The current study aimed to identify the bacteria from the gallbladder, taken during cholecystectomies of patients, by isolating Salmonella typhi and by using microscopic characteristics, biochemical and polymerase chain reaction (PCR) tests. METHODS: A total of 120 specimens were collected from the Baghdad Teaching Hospital, Iraq. A cross-sectional descriptive study was carried out from October, 2021, to July, 2022. During that study, 26 (54.2%) male patient tested positive for Salmonella typhias well as 22 (45.8%) female patients. The age of the patients varied from < 30 to > 60 years. p-value > 0.05 was considered significant to confirm a relationship between age and Salmonella typhi effect for patients. RESULTS: Out of the 120 blood samples taken for this study, 48 (40%) tested positive by use of PCR test, 40 (33.3%) tested positive by use of the Widal test, 35 (29.1%) were positive for biopsy culture, and 35 (29.1%) were positive for blood culture. All Salmonella typhi isolates were found to be sensitive to the imipenem, cefepime, and ceftriaxone, but were resistant to gentamycin, ciprofloxacin, amikacin, erythromycin, and tetracycline (72%, 29%, 43%, 100%, 100%, respectively). CONCLUSIONS: The real time polymerase chain reaction (RT-PCR) tests and the Vitek 2 compact system showed a high level of accuracy in the detection of Salmonella typhi. Multidrug resistance was observed, which should be a signal to reduce antibiotic consumption.

Salmonella Typhi genotypic diversity, cluster identification and antimicrobial resistance determinants in Mukuru settlement, Nairobi Kenya.

BACKGROUND: Understanding the source of typhoid infections and the genetic relatedness of Salmonella Typhi (S. Typhi) by cluster identification in endemic settings is critical for establishing coordinated public health responses for typhoid fever management. This study investigated the genotypic diversity, antibiotic resistance mechanisms, and clustering of 35 S.Typhi strains isolated from cases and carriers in the Mukuru Informal Settlement. METHODS: We studied 35 S.Typhi isolates, including 32 from cases and 3 from carriers, from study participants in the informal settlement of Mukuru, Nairobi, Kenya. Genomic DNA was extracted, and whole-genome sequencing (WGS) was performed to determine the phylogenetic relatedness of strains and detect antimicrobial resistance determinants (AMR). WGS data were analyzed using bioinformatics tools available at the Center for Genomic Epidemiology and Pathogenwatch platforms. RESULTS: Genotype 4.3.1.2 EA3 was found to be dominant at 46% (16/35), followed by 4.3.1.2 EA2 at 28% (10/35), and 4.3.1.1 EA1 at 27% (9/35). A comparison of the isolates with global strains from Pathogenwatch identified close clustering with strains from Uganda, Tanzania, Rwanda, and India. Three isolates (9%) distributed in each cluster were isolated from carriers. All genotype 4.3.1.2 EA3 isolates were genotypically multidrug-resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole. Single mutations in the quinolone resistance-determining region were identified in the gyrA (S83Y) and gyrB (S464F) genes. All isolates associated with multidrug resistance showed the presence of the IncQ1 plasmid with the following genes: blaTEM-1B, catA1, sul1, sul2, and dfrA7. CONCLUSION: The close phylogenetic relatedness between antimicrobial-resistant case isolates and carriage isolates indicates that typhoid carriage is a possible source of infection in the community. Comparative analysis with global isolates revealed that the Kenyan isolates share common lineages with strains from neighboring East African countries and India, suggesting regional dissemination of specific MDR clones. AMR was a major feature of the isolates. Surveillance and testing for antimicrobial susceptibility should inform options for the management of cases.

Extensively Drug-Resistant Salmonella Typhi: A National Disaster.

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Tracking the shift in enteric fever trends and evolving antibiotic sensitivity patterns.

Objective: This study aims to examine the frequency of Salmonella Paratyphi found in blood cultures and evaluate the antibiotic susceptibility pattern of Salmonella isolates to different antibiotics. Additionally, the study aims to assess the paradigm shift in the trend of enteric fever caused by Salmonella Typhi (S. Typhi) to Salmonella Paratyphi(S. Paratyphi) . Study Design: Retrospective study. Participant: The study enrolled patients aged 12 years and above diagnosed with enteric fever (positive blood culture) and admitted to Peelamedu Samanaidu Govindasamy Naidu (PSG) Hospital. Interventions: The study analyzed demographic and antibiotic susceptibility profiles of Salmonella isolates collected from 106 enteric fever patients in the hospital between 2010 and 2022. The susceptibility profiles of Salmonella isolates to multiple antibiotics were assessed. Results: There were 106 participants, and 95 (89.62%) of them had enteric fever linked to Salmonella Typhi, while only 11 (10.38%) had enteric fever linked to Salmonella Paratyphi A. From 2010 to 2022, the study discovered a general decline in the prevalence of enteric fever caused by Salmonella species. But between 2014 and 2022, the incidence of enteric fever linked to S. Typhi rapidly increased. Azithromycin (100% , n = 106) and ceftriaxone (99% , n = 105) were highly effective against the Salmonella isolates, whereas nalidixic acid was resisted by 3 isolates (4.72%, n = 3). Conclusion: The study observed a higher incidence of Salmonella Typhi in comparison to Paratyphi A and a greater susceptibility of males to enteric fever. Funding: None declared.

A portable label-free electrochemical DNA biosensor for rapid detection of Salmonella Typhi.

A highly accurate, rapid, portable, and robust platform for detecting Salmonella enterica serovar Typhi (S. Typhi) is crucial for early-stage diagnosis of typhoid to avert and control the outbreaks of this pathogen, which threaten global public health. This study presents a proof-of-concept for our developed label-free electrochemical DNA biosensor system for S. Typhi detection, which employs a printed circuit board gold electrode (PCBGE), integrated with a portable potentiostat reader. Initially, the functionalized DNA biosensor and target detection were characterized using cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS) methods using a benchtop potentiostat. Interestingly, the newly developed DNA biosensor can identify target single-stranded DNA concentrations ranging from 10 nM to 20 µM, achieving a detection limit of 7.6 nM within a brief 5 minute timeframe. Under optimal detection conditions, the DNA biosensor exhibits remarkable selectivity, capable of distinguishing a single mismatch base pair from the target single-stranded DNA sequence. We then evaluated the feasibility of the developed DNA biosensor system as a diagnostic tool by detecting S. Typhi in 50 clinical samples using a portable potentiostat reader based on the DPV technique. Remarkably, the developed biosensor can distinctly distinguish between positive and negative samples, indicating that the miniaturised DNA biosensor system is practical for detecting S. Typhi in real biological samples. The developed DNA biosensor device in this work proves to be a promising point-of-care (POC) device for Salmonella detection due to its swift detection time, uncomplicated design, and streamlined workflow detection system.

Typhoid and paratyphoid fever epidemiological indicators and spatiotemporal analysis in China from 2004 to 2019.

Typhoid and paratyphoid fever are systemic infections caused by Salmonella Typhi and Salmonella Paratyphi. These diseases are endemic in many parts of China, occurring periodically throughout the year. Epidemiological features, temporal trends, and spatial distribution of these fevers were analyzed using GraphPad Prism 9 with data collected by China's Public Health Science Data Center from 2004 to 2019. Charts were generated to depict their incidence across provinces, years, age groups, and occupations. Spatial clustering was assessed using ArcGIS 10.5 and Moran's I index. SaTScan 9.5 was employed to analyze their spatiotemporal distribution. From 2004 to 2019, China reported 197,623 cases of typhoid fever, resulting in 72 deaths, and 84,583 cases of paratyphoid fever, with 17 fatalities, showing a yearly reduction. Epidemic zones for these diseases are primarily in Yunnan, Guangxi, Guizhou, and other southwestern regions, affecting predominantly peasants and students. Children and adolescents are particularly vulnerable. Due to the epidemic nature of these diseases, they can occur year-round, with peaks in the summer months. This study provides a comprehensive understanding of their epidemiological characteristics and geographic distribution in China, emphasizing the need for authorities to improve living conditions, implement preventive measures, and develop effective treatments and vaccines in these high-risk areas.

Modelling Salmonella Typhi in high-density urban Blantyre neighbourhood, Malawi, using point pattern methods.

Salmonella Typhi is a human-restricted pathogen that is transmitted by the faecal-oral route and causative organism of typhoid fever. Using health facility data from 2016 to 2020, this study focuses on modelling the spatial variation in typhoid risk in Ndirande township in Blantyre. To pursue this objective, we developed a marked inhomogeneous Poisson process model that allows us to incorporate both individual-level and environmental risk factors. The results from our analysis indicate that typhoid cases are spatially clustered, with the incidence decreasing by 54% for a unit increase in the water, sanitation, and hygiene (WASH) score. Typhoid intensity was also higher in children aged below 18 years than in adults. However, our results did not show evidence of a strong temporal variation in typhoid incidence. We also discuss the inferential benefits of using point pattern models to characterise the spatial variation in typhoid risk and outline possible extensions of the proposed modelling framework.

Clinical characteristics of enteric fever and performance of TUBEX TF IgM test in Indonesian hospitals.

BACKGROUND: Accurate diagnosis of enteric fever is challenging, particularly in low- and middle-income countries, due to the overlap of clinical and laboratory features with other pathogens. To better understand the difficulties in enteric fever diagnosis, we evaluated the characteristics of patients clinically diagnosed with enteric fever and the real-world performance of TUBEX TF, one of the most used tests in Indonesia. METHODOLOGY/PRINCIPAL FINDINGS: Patients were recruited through the AFIRE (Etiology of Acute Febrile Illness Requiring Hospitalization) study at eight Indonesian hospitals. Blood culture was performed for all patients, and TUBEX TF was performed for suspected enteric cases. Salmonella PCR and ELISA tests were performed at a reference lab. Sensitivity and specificity of TUBEX TF and IgM and IgG anti-S. Typhi ELISA were determined. Of 301 patients clinically diagnosed with enteric fever, 50 (16.6%) were confirmed by blood culture and/or PCR. Confirmed cases were mostly school-aged children presenting with fever, anorexia, dizziness and/or abdominal pain with normal leukocyte count or leukopenia. TUBEX TF demonstrated a sensitivity of 97.6% to 70.7% and specificity of 38.3% to 67.2% at cutoffs of 4 and 6, respectively. Acute IgG demonstrated the best sensitivity and specificity, at 90.7% and 82.7%, respectively, and the best ROC characteristics. CONCLUSIONS/SIGNIFICANCE: A substantial proportion of enteric fever was misdiagnosed at all study hospitals, likely due to the overlap of clinical characteristics and lab parameters with those of other common pathogens. The TUBEX TF rapid serological assay demonstrated suboptimal performance in our setting and tended to over-diagnose enteric fever. The role of IgG from acute specimens for identification of enteric fever cases merits additional consideration.

The frequency and associated factors of typhoid carriage in patients undergoing cholecystectomy for gallbladder disease in Pakistan: A cross-sectional study.

BACKGROUND: Enteric fever is caused by Salmonella enterica serovars Typhi (S. Typhi) and Paratyphi A, B, and C. It continues to be a significant cause of morbidity and mortality worldwide. In highly endemic areas, children are disproportionately affected, and antimicrobial resistance reduces therapeutic options. It is estimated that 2-5% of enteric fever patients develop chronic asymptomatic infection. These carriers may act as reservoirs of infection; therefore, the prospective identification and treatment of carriers are critical for long-term disease control. We aimed to find the frequency of Salmonella Typhi carriers in patients undergoing cholecystectomy. We also compared the detection limit of culturing versus qPCR in detecting S. Typhi, performed a geospatial analysis of the carriers identified using this study, and evaluated the accuracy of anti-Vi and anti-YncE in identifying chronic typhoid carriage. METHODS: We performed a cross-sectional study in two centers in Pakistan. Gallbladder specimens were subjected to quantitative PCR (qPCR) and serum samples were analyzed for IgG against YncE and Vi by ELISA. We also mapped the residential location of those with a positive qPCR result. FINDINGS: Out of 988 participants, 3.4% had qPCR-positive gallbladder samples (23 S. Typhi and 11 S. Paratyphi). Gallstones were more likely to be qPCR positive than bile and gallbladder tissue. Anti-Vi and YncE were significantly correlated (r = 0.78 p<0.0001) and elevated among carriers as compared to qPCR negative controls, except for anti-Vi response in Paratyphi A. But the discriminatory values of these antigens in identifying carriers from qPCR negative controls were low. CONCLUSION: The high prevalence of typhoid carriers observed in this study suggests that further studies are required to gain information that will help in controlling future typhoid outbreaks in a superior manner than they are currently being managed.

Primary Aortoenteric Fistula Due to Salmonella typhi-related Mycotic Aneurysm.

Primary aortoenteric fistulas (AEF) are rare. The majority of these are due to atherosclerotic aortic aneurysms. Mycotic aortic aneurysms leading to primary AEF are exceedingly uncommon. Here we report a rare case of primary AEF secondary to Salmonella-related mycotic aneurysm and discuss the diagnostic and therapeutic issues.

Case Report: Salmonella typhi Iliopsoas Abscess with Concomitant Sacroiliitis in a Young Immunocompetent Male: A Rare Case.

Iliopsoas abscess is an infrequent condition characterized by the collection of pus in the iliopsoas compartment. The prevalence of the disease has been increasing in recent years with the emergence of various comorbidities and risk factors. The availability of newer imaging modalities has also improved the detection of new cases. Salmonellosis is an uncommon etiology in iliopsoas abscess and sacroiliitis. Most cases reported in the literature are associated with Staphylococcus aureus, Streptococci species, and Escherichia coli. Diabetes, hematological malignancies, HIV, and other immunocompromised states are important comorbidities/risk factors for iliopsoas abscess. We report a case of an 18-year-old male who presented with a history of fever and right hip pain for 10 days. Radioimaging revealed right sacroiliitis and iliopsoas abscess. Blood culture revealed pan-sensitive Salmonella typhi. After the prolonged course of antibiotics (intravenous ceftriaxone followed by oral levofloxacin), the patient improved with no further relapse in symptoms. Salmonella typhi should be an important differential of iliopsoas abscess in endemic regions after ruling out the common etiology such as S. aureus and Mycobacterium tuberculosis.

Epidemiology of non-travel enteric fever cases in England: insights from 10 years of surveillance.

OBJECTIVES: In non-endemic countries, surveillance of non-travel cases of enteric fever is important to identify carriers and reduce secondary transmission. We characterised these cases in England between 2012 and 2021 and assessed potential sources of infection to inform guidance revision. STUDY DESIGN: Retrospective case-case. METHODS: We identified enteric fever cases from the national surveillance dataset. Non-travel cases were defined as no travel to an endemic country or travel but onset of >60 days after return. Multivariable logistic regression was used to identify factors associated with non-travel cases. We reviewed the case records of cases with unknown source of infection. RESULTS: Compared to travel cases, non-travel cases (7%; 225/3075) were older (odds ratio [OR] = 1.02, 95% confidence interval [CI]: 1.02-1.04), asymptomatic (OR = 9.3: 95% CI: 4.3-20.3), and confirmed with Salmonella typhi infection (OR = 1.74, 95% CI: 1.26-2.4). Non-travel cases had lower odds of being of Indian (OR = 0.27, 95% CI: 0.16-0.45) or Pakistani ethnicity (OR = 0.34, 95% CI: 0.16-0.45) than White British. Surveillance questionnaires identified a possible infection source for 53%: case records review identified a further 23%: 33% secondary transmission, mostly household; 21% had overseas visitors, or travelling family; 12% were carriers (cases with enteric fever in the past), 12% travelled to endemic country outside of the 60-day window, and 22% had other possible sources. Case records differentiated between travel 60-90 days (5%) vs travel years prior to onset (7%), suggesting carrier status. CONCLUSION: Not all possible carriers were identified through the surveillance questionnaire. Therefore, we recommend additional questions to systematically capture travel history beyond 60 days to assist in classifying carrier status and to updating the source of infection.

Development, confirmation, and application of a seeded Escherichia coli process control organism to validate Salmonella enterica serovar Typhi environmental surveillance methods.

Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of Typhoid fever. Blood culture is the gold standard for clinical diagnosis, but this is often difficult to employ in resource limited settings. Environmental surveillance of waste-impacted waters is a promising supplement to clinical surveillance, however validating methods is challenging in regions where S. Typhi concentrations are low. To evaluate existing S. Typhi environmental surveillance methods, a novel process control organism (PCO) was created as a biosafe surrogate. Using a previous described qPCR assay, a modified PCR amplicon for the staG gene was cloned into E. coli. We developed a target region that was recognized by the Typhoid primers in addition to a non-coding internal probe sequence. A multiplex qPCR reaction was developed that differentiates between the typhoid and control targets, with no cross-reactivity or inhibition of the two probes. The PCO was shown to mimic S. Typhi in lab-based experiments with concentration methods using primary wastewater: filter cartridge, recirculating Moore swabs, membrane filtration, and differential centrifugation. Across all methods, the PCO seeded at 10 CFU/mL and 100 CFU/mL was detected in 100% of replicates. The PCO is detected at similar quantification cycle (Cq) values across all methods at 10 CFU/mL (Average = 32.4, STDEV = 1.62). The PCO was also seeded into wastewater at collection sites in Vellore (India) and Blantyre (Malawi) where S. Typhi is endemic. All methods tested in both countries were positive for the seeded PCO. The PCO is an effective way to validate performance of environmental surveillance methods targeting S. Typhi in surface water.

Trends in typhoid fever during the COVID-19 pandemic in Pakistan.

INTRODUCTION: Pakistan has been experiencing an extensively drug-resistant (XDR) outbreak of typhoid for some years. We sought to evaluate how the COVID-19 pandemic impacted typhoid epidemiology in Pakistan, from the beginning of the pandemic in 2020 through the end of 2022, and the reduction of COVID-19 cases. METHODOLOGY: We compared national public COVID-19 data with retrospectively obtained patient data of confirmed S. Typhi isolates between January 2019 and December 2022 from Shaukat Khanum Memorial Cancer Hospital and Research Centre and the hospital's extended network of laboratory collection centers across Pakistan. RESULTS: We observed that during the early onset of the COVID-19 pandemic and COVID-19 peaks, typhoid positivity generally decreased. This suggests that restrictions and non-pharmaceutical interventions that limited social interactions and promoted good sanitation and hygiene practices had a positive secondary effect on typhoid. This led to an overall yearly decrease in typhoid positivity between 2019 to 2021. However, the percentage of S. Typhi cases isolated that were ceftriaxone-resistant continued to increase, suggesting the continued dominance of XDR typhoid in Pakistan. In 2022, with the alleviation of pandemic restrictions, we observed increased typhoid positivity and COVID-19 and typhoid positivity started to follow similar trends. CONCLUSIONS: Given the continued presence of COVID-19 along with XDR typhoid in Pakistan, it will be imperative to use differential testing to ensure that the epidemiology of each reported is accurate, the spread of each it contained, and that antibiotics are not misused. The use of approved vaccinations will lessen the burden of both diseases.

Ultrasensitive detection of Salmonella typhi using a PAM-free Cas14a-based biosensor.

The effectiveness of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas14a1, widely utilized for pathogenic microorganism detection, has been limited by the requirement of a protospacer adjacent motif (PAM) on the target DNA strands. To overcome this limitation, this study developed a Single Primer isothermal amplification integrated-Cas14a1 biosensor (SPCas) for detecting Salmonella typhi that does not rely on a PAM sequence. The SPCas biosensor utilizes a novel primer design featuring an RNA-DNA primer and a 3'-biotin-modified primer capable of binding to the same single-stranded DNA (ssDNA) in the presence of the target gene. The RNA-DNA primer undergoes amplification and is blocked at the biotin-modified end. Subsequently, strand replacement is initiated to generate ssDNA assisted by RNase H and Bst enzymes, which activate the trans-cleavage activity of Cas14a1 even in the absence of a PAM sequence. Leveraging both cyclic chain replacement reaction amplification and Cas14a1 trans-cleavage activity, the SPCas biosensor exhibits a remarkable diagnostic sensitivity of 5 CFU/mL. Additionally, in the assessment of 20 milk samples, the SPCas platform demonstrated 100% diagnostic accuracy, which is consistent with the gold standard qPCR. This platform introduces a novel approach for developing innovative CRISPR-Cas-dependent biosensors without a PAM sequence.