Typhoid fever

Typhoid fever is an invasive bacterial disease associated with bloodstream infection that causes a high burden of disease in Africa and Asia. Typhoid primarily affects individuals ranging from infants through to young adults. The causative organism, Salmonella enterica subsp. enterica serovar Typhi is transmitted via the faecal-oral route, crossing the intestinal epithelium and disseminating to systemic and intracellular sites, causing an undifferentiated febrile illness. Blood culture remains the practical reference standard for diagnosis of typhoid fever, where culture testing is available, but novel diagnostic modalities are an important priority under investigation. Since 2017, remarkable progress has been made in defining the global burden of both typhoid fever and antimicrobial resistance; in understanding disease pathogenesis and immunological protection through the use of controlled human infection; and in advancing effective vaccination programmes through strategic multipartner collaboration and targeted clinical trials in multiple high-incidence priority settings. This Primer thus offers a timely update of progress and perspective on future priorities for the global scientific community.

gyrA ser83 mutation among fluoroquinolone-resistant Salmonella enterica serovars from enteric fever patients in tertiary care hospital, Kathmandu

BACKGROUND

The management of enteric fever through antibiotics is difficult these days due to the emerging resistance of Salmonella to various antimicrobial agents. The development of antimicrobial resistance is associated with multiple factors including mutations in the specific genes. To know the current status of mutation-mediated fluoroquinolone-resistance among Salmonella enterica serovars; Typhi, Paratyphi A, B and C, this study was focused on detecting gyrA ser83 mutation by restriction digestion analysis of gyrA gene using HinfI endonuclease.

RESULTS

A total of 948 blood samples were processed for isolation of Salmonella spp. and 3.4% of them were found to be positive for Salmonella growth. Out of the 32 Salmonella isolates, 2.2% were S. Typhi and 1.2% were S. Paratyphi A. More interestingly, we observed less than 5% of isolates were resistant to first-line drugs including chloramphenicol, cotrimoxazole and ampicillin. More than 80% of isolates were resistant to fluoroquinolones accounting for 84.4% to levofloxacin followed by 87.5% to ofloxacin and 100% to ciprofloxacin by disc diffusion methods. However, the minimum inhibitory concentration method using agar dilution showed only 50% of isolates were resistant to ciprofloxacin. A total of 3.1% of isolates were multidrug-resistant. Similarly, 90.6% of the Salmonella isolates showed gyrA ser83 mutation with resistance to nalidixic acid.

CONCLUSIONS

The increased resistance to fluoroquinolones and nalidixic acid in Salmonella isolates in our study suggests the use of alternative drugs as empirical treatment. Rather, the treatment should focus on prescribing first-line antibiotics since we observed less than 5% of Salmonella isolates were resistant to these drugs.

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.

Prevalence, probability, and outcomes of typhoidal/non-typhoidal Salmonella and malaria co-infection among febrile patients: a systematic review and meta-analysis

The geographical overlaps of malaria parasites and Salmonella spp. can lead to co-infection of these two pathogens, especially in the tropics where malaria is endemic. Moreover, few literatures suggested that malaria infection was associated with Salmonella bacteremia. Therefore, this study quantified pooled prevalence of typhoidal/non-typhoidal Salmonella (NTS) and probability of typhoidal/NTS and malaria co-infection among febrile patients. The systematic review protocol was registered at PROSPERO (CRD42021252322). Studies on co-infection of typhoidal/NTS and malaria were searched in PubMed, Scopus, and Web of Science. The risk of bias of the included studies was assessed using the checklist for analytical cross-sectional studies developed by the Joanna Briggs Institute. Meta-analyses on the following criteria were performed: (1) pooled prevalence of typhoidal/NTS and malaria co-infection among febrile patients, (2) pooled prevalence of typhoidal/NTS among malaria patients, (3) pooled prevalence of malaria infections among patients with Salmonella spp. infection, and (4) probability of typhoidal/NTS and malaria co-infection among febrile patients. Additionally, the case fatality rate and mean difference of malarial parasitemia between typhoidal/NTS and malaria co-infection and Plasmodium monoinfection were also determined. The subgroup analyses of typhoidal/NTS, regions (Africa and Asia), countries, time (publication year), characteristics of participants, and diagnostic tests for identifying Salmonella spp. were also conducted. A sensitivity test was performed to determine the robustness of the study outcomes. Publication bias among the included studies was evaluated using the funnel plot and Egger’s test. All analyses were performed using Stata version 15 (StataCorp LLC, Texas, USA) with a p-value < 0.05 indicating statistical significance. Eighty-one studies that met the eligibility criteria were included in the analyses. Of the 73,775 study participants, 4523 had typhoidal/NTS and malaria co-infections. The pooled prevalence rates of typhoidal/NTS and malaria co-infection among febrile patients were 14% (95% confidence interval [CI], 9–19%; I², 99.4%; 2971/17,720 cases) and 1% (95% CI 1–1%; I², 89.9%; 252/29,081 cases) using the Widal test and culture methods for identifying Salmonella spp., respectively. The pooled prevalence rates of typhoidal/NTS infection among patients with malaria were 31% (95% CI 23–39%; I², 99.5%; 3202/19,208 cases) and 3% (95% CI 2–3%; I², 86.8%; 407/40,426 cases) using the Widal test and culture methods for identifying Salmonella spp., respectively. The pooled prevalence rates of malaria infection among patients with typhoidal/NTS were 17% (95% CI 6–29%; I², 33.3%; 13/75 cases) and 43% (95% CI 32–53%; I², 89.1%; 287/736 cases), respectively. Malaria infection was associated with typhoidal/NTS in children aged < 15 years (p < 0.0001; odds ratio, 0.36; 95% CI 0.23–0.58; I², 73.9%; 3188/43,212 cases). The case fatality rate in patients with malaria and NTS co-infections was 16% (95% CI 9–24%; I², 89.1%; 18/103 cases). From the view of the present study, the inappropriate use of the Widal test for Salmonella spp. diagnosis can overestimate the prevalence of typhoidal/NTS and malaria co-infections. Malaria infection associated with typhoidal/NTS in children and the high case fatality rates among few patients with co-infections were highlighted. Future prospective longitudinal studies using the appropriate and confirmatory dsiagnosis for Salmonella spp. infections are highly recommended to ensure the real prevalence of co-infection and highlight the outcome of co-infection for providing adequate treatment in febrile patients who live in areas where malaria is endemic, such as tropical Africa and India.

Two-Color Duplex Platform for Point-of-Care Differential Detection of Malaria and Typhoid Fever

Malaria and typhoid fever are two febrile illnesses prevalent in the tropics that often present overlapping symptoms. In this work, we demonstrate an optical reader-based diagnostics platform for rapid codetection and quantification of two antigen targets: lipopolysaccharide (LPS) for typhoid fever and plasmodium lactate dehydrogenase (pLDH) for malaria infections. We report a limit of detection (LoD) of 5 ng/mL for LPS and 10 ng/mL for pLDH in a spiked serum test. We also validated the duplex test's performance of differentiating malaria infection, typhoid fever infection, and coinfection by testing clinical samples in human serum. Our platform provides the potential for further multiplexing by encoding different color codes to various detection targets. The rapid result (∼15 min), low cost (∼$2), and minimal volume requirement for human serum clinical samples (4 μL) of our diagnostic platform offer great potential for deployment in resource-limited settings to help distinguish common causes for acute febrile illnesses at the point-of-need.

Detection of multidrug-resistant Salmonella enterica subsp. enterica serovar Typhi isolated from Iraqi subjects

Background and Aim

Enteric fever initiated by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi) is among the most consistent disease worldwide, particularly in developing countries. The present study aimed to isolate and identify S. Typhi from typhoid suspected patients and determine their antibacterial susceptibility testing.

Materials and Methods

Thirty blood samples were collected from typhoid suspected patients in Baghdad, Iraq. The samples were cultured on SS agar and XLD agar for screening of S. Typhi. The suspected colonies were picked up and subjected to Vitek 2 compact for biochemical identification and antibacterial susceptibility testing of the organisms. Molecular identification of the isolates was performed by real-time polymerase chain reaction (RT-PCR).

Results

Black colonies were observed on cultured plates. Out of 30 samples, 27 and 29 isolates were identified as S. Typhi using Vitek 2 compact and RT-PCR, respectively. The data of the present study revealed that the strains of S. Typhi were showing multidrug resistance. All S. Typhi strains exhibited resistance to penicillins (ticarcillin and piperacillin), cephalosporins 4^th G (cefepime), and monobactam (aztreonam). However, all the strains showed susceptibility against carbapenems (imipenem and meropenem) and tetracycline (minocycline).

Conclusion

RT-PCR and Vitek 2 compact showed a high level of accuracy in the detection of S. Typhi. Multidrug resistance was observed, which is an alert for the reduction of antibiotic consumption.

Designing a typhoid environmental surveillance study: A simulation model for optimum sampling site allocation

Environmental surveillance can be used for monitoring enteric disease in a population by detecting pathogens, shed by infected people, in sewage. Detection of pathogens depends on many factors: infection rates and shedding in the population, pathogen fate in the sewerage network, and also sampling sites, sample size, and assay sensitivity. This complexity makes the design of sampling strategies challenging, which creates a need for mathematical modeling to guide decision making.

In the present study, a model was developed to simulate pathogen shedding, pathogen transport and fate in the sewerage network, sewage sampling, and detection of the pathogen. The simulation study used Salmonella enterica serovar Typhi (S. Typhi) as the target pathogen and two wards in Kolkata, India as the study area. Five different sampling strategies were evaluated for their sensitivity of detecting S. Typhi, by sampling unit: sewage pumping station, shared toilet, adjacent multiple shared toilets (primary sampling unit), pumping station + shared toilets, pumping station + primary sampling units. Sampling strategies were studied in eight scenarios with different geographic clustering of risk, pathogen loss (decay, leakage), and sensitivity of detection assays. A novel adaptive sampling site allocation method was designed, that updates the locations of sampling sites based on their performance. We then demonstrated how the simulation model can be used to predict the performance of environmental surveillance and how it is improved by optimizing the allocation of sampling sites.

The results are summarized as a decision tree to guide the sampling strategy based on disease incidence, geographic distribution of risk, pathogen loss, and the sensitivity of the detection assay. The adaptive sampling site allocation method consistently outperformed alternatives with fixed site locations in most scenarios. In some cases, the optimum allocation method increased the median sensitivity from 45% to 90% within 20 updates.

Clinical Evaluation of a Multiplex PCR for the Detection of Salmonella enterica Serovars Typhi and Paratyphi A from Blood Specimens in a High-Endemic Setting

Enteric fever is a major public health concern in endemic areas, particularly in infrastructure-limited countries where Salmonella Paratyphi A has emerged in increasing proportion of cases. We aimed to evaluate a method to detect Salmonella Typhi (S. Typhi) and Salmonella Paratyphi A (S. Paratyphi A) in febrile patients in Bangladesh. We conducted a prospective study enrolling patients with fever > 38°C admitted to two large urban hospitals and two outpatient clinics located in Dhaka, Bangladesh. We developed and evaluated a method combining short culture with a new molecular assay to simultaneously detect and differentiate S. Typhi and S. Paratyphi A from other Salmonella directly from 2 to 4 mL of whole blood in febrile patients (n = 680). A total of 680 cases were enrolled from the four participating sites. An increase in the detection rate (+38.8%) in S. Typhi and S. Paratyphi A was observed with a multiplex polymerase chain reaction (PCR) assay, and absence of non-typhoidal Salmonella detection was reported. All 45 healthy controls were culture and PCR negative, generating an estimated 92.9% of specificity on clinical samples. When clinical performance was assessed in the absence of blood volume prioritization for testing, a latent class model estimates clinical performance ≥ 95% in sensitivity and specificity with likelihood ratio (LR) LR+ > 10 and LR− < 0.1 for the multiplex PCR assay. The alternative method to blood culture we developed may be useful alone or in combination with culture or serological tests for epidemiological studies in high disease burden settings and should be considered as secondary endpoint test for future vaccine trials.

A cross-sectional study of enteric fever among febrile patients at Ambo hospital: prevalence, risk factors, comparison of Widal test and stool culture and antimicrobials susceptibility pattern of isolates

Background

Enteric fever is one of the common infectious diseases of humans. The objectives of this study were to:1) estimate the prevalence of enteric fever among febrile patients visiting Ambo hospital; 2) comparison of Widal test and stool culture;3) evaluation of the antimicrobial susceptibility of isolates; and 4) assess potential risk factors to acquire enteric fever infection.

Methods

Blood and stool samples were collected from 372 febrile patients with symptoms clinically similar to enteric fever. Widal test was used for testing sera while stool culturing and bacterial identification was done using WHO standard methods. Susceptibility testing was done using Kirby-Bauer disc diffusion method. Chi-Square test and Logistic Regression analysis were used to analyze the data.

Results

The apparent and true prevalence of enteric fever were 56.2% (95% confidence interval [CI]: 50.97–61.29%) and 57.52% (95% CI: 52.3–62.6%) respectively, while, the culture prevalence was 2.7% (95% CI: 1.30–4.89%). Isolation rates of S. Typhi and S. Paratyphi were 0.8% (95% CI: 0.17–2.34%) and 1.9% (95% CI: 0.76–3.84%) respectively. The isolates showed 100% resistance to amoxicillin, bacitracin, erythromycin, 80%resistance to cefotaxime and streptomycin and 20% for chloramphenicol. The sensitivity, specificity, positive and negative predictive values of Widal test was 80.0, 44.5, 3.8 and 98.8% respectively. Multivariable logistic regression analysis revealed that age (adjusted odds ratio [aOR] = 2.45; 95% CI: 1.38–4.37; P = 0.002), religion (aOR = 15.57, 95% CI: 3.01–80.64; P = 0.001), level of education (aOR = 2.60, 95% CI: 1.27–5.28; P = 0.009), source of water (aOR = 2.20, 95% CI: 1.21–3.98; P = 0.009), raw milk (aOR =2.19, 95% CI:1.16–4.16; P = 0.016) and raw meat consumption (aOR = 1.80, 95% CI: 1.07–3.01; P = 0.026) are the predictors of enteric fever seropositivity.

Conclusions

Patients were wrongly diagnosed and treated for enteric fever by Widal test. Therefore, rapid tests with better sensitivity and specificity are needed for the diagnosis of enteric fever. Provision of safe water and health education are vital to bring behavioral change towards raw food consumption.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3917-3) contains supplementary material, which is available to authorized users.

The Relationship Between Blood Sample Volume and Diagnostic Sensitivity of Blood Culture for Typhoid and Paratyphoid Fever: A Systematic Review and Meta-Analysis

Background

Blood culture is the standard diagnostic method for typhoid and paratyphoid (enteric) fever in surveillance studies and clinical trials, but sensitivity is widely acknowledged to be suboptimal. We conducted a systematic review and meta-analysis to examine sources of heterogeneity across studies and quantified the effect of blood volume.

Methods

We searched the literature to identify all studies that performed blood culture alongside bone marrow culture (a gold standard) to detect cases of enteric fever. We performed a meta-regression analysis to quantify the relationship between blood sample volume and diagnostic sensitivity. Furthermore, we evaluated the impact of patient age, antimicrobial use, and symptom duration on sensitivity.

Results

We estimated blood culture diagnostic sensitivity was 0.59 (95% confidence interval [CI], 0.54-0.64) with significant between-study heterogeneity (I2, 76% [95% CI, 68%-82%]; P < .01). Sensitivity ranged from 0.51 (95% CI, 0.44-0.57) for a 2-mL blood specimen to 0.65 (95% CI, 0.58-0.70) for a 10-mL blood specimen, indicative of a relationship between specimen volume and sensitivity. Subgroup analysis showed significant heterogeneity by patient age and a weak trend towards higher sensitivity among more recent studies. Sensitivity was 34% lower (95% CI, 4%-54%) among patients with prior antimicrobial use and 31% lower after the first week of symptoms (95% CI, 19%-41%). There was no evidence of confounding by patient age, antimicrobial use, symptom duration, or study date on the relationship between specimen volume and sensitivity.

Conclusions

The relationship between the blood sample volume and culture sensitivity should be accounted for in incidence and next-generation diagnostic studies.

Introductory Article on Global Burden and Epidemiology of Typhoid Fever

This article is the introduction to a 12-paper supplement on global trends in typhoid fever. The Tackling Typhoid (T2) project was initiated in 2015 to synthesize the existing body of literature on typhoidal salmonellae and study national and regional typhoid fever trends. In addition to a global systematic review, eight case studies were undertaken to examine typhoid and paratyphoid fever trends in endemic countries alongside changes in relevant contextual factors. Incidence variations exist both within and between regions with large subnational differences as well, suggesting that public health changes impacting typhoid and paratyphoid fevers in one setting may not have similar impacts in another. This supplement also brings to light the lack of national typhoid fever surveillance systems, inconsistencies in diagnostics, and the lack of typhoid fever associated morbidity and mortality data in many countries, making it difficult to accurately quantify and track burden of disease. To better understand typhoid fever there is a need for more high-quality data from resource-poor settings. The implementation of typhoid surveillance systems alongside the transition to blood-culture confirmation of cases, where possible, would aid in the improvement of data quality in low-income settings. The following supplement includes the results of our global systematic review, eight-country case study articles, a qualitative article informed by semistructured interviews, and a conclusion article on potential ways forward for typhoid control.

Typhoid fever: issues in laboratory detection, treatment options & concerns in management in developing countries

Multidrug-resistant Salmonella enterica subsp. enterica serovar Typhi (resistant to ampicillin, chloramphenicol and cotrimoxazole), was significantly reduced with the increased usage of fluoroquinolones and azithromycin. This has led to declining multidrug resistance rates in India with increasing ciprofloxacin nonsusceptibility rates and clinical failures due to azithromycin. However, for the available agents such as ceftriaxone, azithromycin and fluoroquinolones, the dose and duration for treatment is undefined. The ongoing clinical trials for typhoid management are expected to recommend the defined dose and duration for better clinical outcome. We made an attempt to summarize the issues in laboratory detection, treatment options and responses, and the concerns in clinical practice seen in the developing countries.

Typhoid fever is an important cause of mortality in developing countries and is a major public health concern. Cephalosporins or azithromycin are the drugs of choice for treating infection caused by the reduced fluoroquinolone susceptibility of S. Typhi. Emergence of cephalosporin resistance in S. Typhi and azithromycin-associated clinical and microbiological failure is of significant concern in developing countries. An approach of cephalosporin–azithromycin combination therapy has been suggested, which could be a potential alternative in treating uncomplicated S. Typhi infection in endemic areas. This review summarizes the field so far.

Modifiable risk factors for typhoid intestinal perforations during a large outbreak of typhoid fever, Kampala Uganda, 2015

Background

Between January and June, 2015, a large typhoid fever outbreak occurred in Kampala, Uganda, with 10,230 suspected cases. During the outbreak, area surgeons reported a surge in cases of typhoid intestinal perforation (TIP), a complication of typhoid fever. We conducted an investigation to characterize TIP cases and identify modifiable risk factors for TIP.

Methods

We defined a TIP case as a physician-diagnosed typhoid patient with non-traumatic terminal ileum perforation. We identified cases by reviewing medical records at all five major hospitals in Kampala from 2013 to 2015. In a matched case-control study, we compared potential risk factors among TIP cases and controls; controls were typhoid patients diagnosed by TUBEX TF, culture, or physician but without TIP, identified from the outbreak line-list and matched to cases by age, sex and residence. Cases and controls were interviewed using a standard questionnaire from 1st -23rd December 2015. We used conditional logistic regression to assess risk factors for TIP and control for confounding.

Results

Of the 88 TIP cases identified during 2013–2015, 77% (68/88) occurred between January and June, 2015; TIPs sharply increased in January and peaked in March, coincident with the typhoid outbreak. The estimated risk of TIP was 6.6 per 1000 suspected typhoid infections (68/10,230). The case-fatality rate was 10% (7/68). Cases sought care later than controls; Compared with 29% (13/45) of TIP cases and 63% (86/137) of controls who sought treatment within 3 days of onset, 42% (19/45) of cases and 32% (44/137) of controls sought treatment 4–9 days after illness onset (OR_adj = 2.2, 95%CI = 0.83–5.8), while 29% (13/45) of cases and 5.1% (7/137) of controls sought treatment ≥10 days after onset (OR_adj = 11, 95%CI = 1.9–61). 68% (96/141) of cases and 23% (23/100) of controls had got treatment before being treated at the treatment centre (OR_adj = 9.0, 95%CI = 1.1–78).

Conclusion

Delay in seeking treatment increased the risk of TIPs. For future outbreaks, we recommended aggressive community case-finding, and informational campaigns in affected communities and among local healthcare providers to increase awareness of the need for early and appropriate treatment.

Molecular diagnosis of Salmonella typhi and its virulence in suspected typhoid blood samples through nested multiplex PCR

A nested multiplex polymerase chain reaction (PCR) based diagnosis was developed for the detection of virulent Salmonella typhi in the blood specimens from patients suspected for typhoid fever. After the Widal test, two pairs of primers were used for the detection of flagellin gene (fliC) of S. typhi. Among them, those positive for fliC alone were subjected to identification of genes in Via B operon of Salmonella Pathogenesity Island (SPI-7) where four primer pairs were used to detect tviA and tviB genes. Among 250 blood samples tested, 115 were positive by fliC PCR; 22 of these were negative for tviA and tviB. Hence, the method described here can be used to diagnose the incidence of Vi-negative serovar typhi especially in endemic regions where the Vi vaccine is administered.

Blood culture-PCR to optimise typhoid fever diagnosis after controlled human infection identifies frequent asymptomatic cases and evidence of primary bacteraemia

Background

Improved diagnostics for typhoid are needed; a typhoid controlled human infection model may accelerate their development and translation. Here, we evaluated a blood culture-PCR assay for detecting infection after controlled human infection with S. Typhi and compared test performance with optimally performed blood cultures.

Methodology/Principal findings

Culture-PCR amplification of blood samples was performed alongside daily blood culture in 41 participants undergoing typhoid challenge. Study endpoints for typhoid diagnosis (TD) were fever and/or bacteraemia. Overall, 24/41 (59%) participants reached TD, of whom 21/24 (86%) had ≥1 positive blood culture (53/674, 7.9% of all cultures) or 18/24 (75%) had ≥1 positive culture-PCR assay result (57/684, 8.3%). A further five non-bacteraemic participants produced culture-PCR amplicons indicating infection; overall sensitivity/specificity of the assay compared to the study endpoints were 70%/65%. We found no significant difference between blood culture and culture-PCR methods in ability to identify cases (12 mismatching pairs, p = 0.77, binomial test). Clinical and stool culture metadata demonstrated that additional culture-PCR amplification positive individuals likely represented true cases missed by blood culture, suggesting the overall attack rate may be 30/41 (73%) rather than 24/41 (59%). Several participants had positive culture-PCR results soon after ingesting challenge providing new evidence for occurrence of an early primary bacteraemia.

Conclusions/Significance

Overall the culture-PCR assay performed well, identifying extra typhoid cases compared with routine blood culture alone. Despite limitations to widespread field-use, the benefits of increased diagnostic yield, reduced blood volume and faster turn-around-time, suggest that this assay could enhance laboratory typhoid diagnostics in research applications and high-incidence settings.

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Culture in ox-bile/tryptone soy broth selectively enriches for bile-tolerant Salmonella Typhi while lysing human cells.

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PCR sensitivity for detecting typhoid in clinical blood is limited by very low level bacteraemia during clinical illness.

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PCR amplification of S. Typhi fliC-d in pre-cultured blood can accurately identify typhoid infection in challenge study participants.

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Daily culture-PCR of blood collected from challenge study participants suggests primary bacteraemia occurs 12–36 h after S. Typhi ingestion.

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Additional use of culture-PCR demonstrates the true attack rate after typhoid challenge is markedly higher (75%) than previously assumed (60%).

Challenges and Opportunities for Typhoid Fever Control: A Call for Coordinated Action

The burden of enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi is substantial and has high impact in toddlers and young children. This burden is relatively well documented in Asia, and this supplement provides new data on the substantial burden in several sub-Saharan African countries. Challenges in standardized surveillance and imperfect diagnostic tools have resulted in patchy local disease data, which are not well acknowledged or integrated into local country evidence and health awareness for decision making. There is a need to strengthen diagnostics for the generation of burden data in country. Furthermore, the guidelines and training for treatment of enteric fever cases in Africa are sorely needed to help mitigate the inappropriate use of antimicrobial treatment. Classic water safety and access to sanitation development remain powerful tools for the control of typhoid fever, yet the huge economic costs and long timelines are unlikely to provide a short- to middle-term solution. Emerging threats, including multidrug resistance and increasing urbanization in regions such as sub-Saharan Africa, warrant focused attention to shorter-term interventions including immunization, and must include vaccine strategies with the new typhoid conjugate vaccines.

Detection of Typhoidal and Paratyphoidal Salmonella in Blood by Real-time Polymerase Chain Reaction

BACKGROUND

The gold standard for diagnosis of enteric fever caused by Salmonella Typhi or Salmonella Paratyphi A or B is bone marrow culture. However, because bone marrow aspiration is highly invasive, many hospitals and large health centers perform blood culture instead. As blood culture has several limitations, there is a need for novel typhoid diagnostics with improved sensitivity and more rapid time to detection.

METHODS

We developed a clyA-based real-time polymerase chain reaction (qPCR) method to detect Salmonella Typhi and Salmonella Paratyphi A simultaneously in blood. The sensitivity and specificity of this probeset was first evaluated in vitro in the laboratory and then in a typhoid-endemic population, in Karachi, Pakistan, and in healthy US volunteers.

RESULTS

We optimized a DNA extraction and real-time PCR-based method that could reliably detect 1 colony-forming unit/mL of Salmonella Typhi. The probe set was able to detect clinical Salmonella Typhi and Salmonella Paratyphi A strains and also diarrheagenic Escherichia coli, but not invasive E. coli or other invasive bacteria. In the field, the clyA qPCR diagnostic was 40% as sensitive as blood culture. However, when qPCR-positive specimens were considered to be true positives, blood culture only exhibited 28.57% sensitivity. Specificity was ≥90% for all comparisons and in the healthy US volunteers. qPCR was significantly faster than blood culture in terms of detection of typhoid and paratyphoid.

CONCLUSIONS

Based on lessons learned, we recommend that future field trials of this and other novel diagnostics that detect typhoidal and nontyphoidal Salmonella employ multiple methodologies to define a "positive" sample.

What proportion of Salmonella Typhi cases are detected by blood culture? A systematic literature review

Blood culture is often used in definitive diagnosis of typhoid fever while, bone marrow culture has a greater sensitivity and considered reference standard. The sensitivity of blood culture measured against bone marrow culture results in measurement bias because both tests are not fully sensitive. Here we propose a combination of the two cultures as a reference to define true positive S. Typhi cases. Based on a systematic literature review, we identified ten papers that had performed blood and bone marrow culture for S. Typhi in same subjects. We estimated the weighted mean of proportion of cases detected by culture measured against true S. Typhi positive cases using a random effects model. Of 529 true positive S. Typhi cases, 61 % (95 % CI 52–70 %) and 96 % (95 % CI 93–99 %) were detected by blood and bone marrow cultures respectively. Blood culture sensitivity was 66 % (95 % CI 56–75 %) when compared with bone marrow culture results. The use of blood culture sensitivity as a proxy measure to estimate the proportion of typhoid fever cases detected by blood culture is likely to be an underestimate. As blood culture sensitivity is used as a correction factor in estimating typhoid disease burden, epidemiologists and policy makers should account for the underestimation.

A Meta-Analysis of Typhoid Diagnostic Accuracy Studies: A Recommendation to Adopt a Standardized Composite Reference

Novel typhoid diagnostics currently under development have the potential to improve clinical care, surveillance, and the disease burden estimates that support vaccine introduction. Blood culture is most often used as the reference method to evaluate the accuracy of new typhoid tests; however, it is recognized to be an imperfect gold standard. If no single gold standard test exists, use of a composite reference standard (CRS) can improve estimation of diagnostic accuracy. Numerous studies have used a CRS to evaluate new typhoid diagnostics; however, there is no consensus on an appropriate CRS. In order to evaluate existing tests for use as a reference test or inclusion in a CRS, we performed a systematic review of the typhoid literature to include all index/reference test combinations observed. We described the landscape of comparisons performed, showed results of a meta-analysis on the accuracy of the more common combinations, and evaluated sources of variability based on study quality. This wide-ranging meta-analysis suggests that no single test has sufficiently good performance but some existing diagnostics may be useful as part of a CRS. Additionally, based on findings from the meta-analysis and a constructed numerical example demonstrating the use of CRS, we proposed necessary criteria and potential components of a typhoid CRS to guide future recommendations. Agreement and adoption by all investigators of a standardized CRS is requisite, and would improve comparison of new diagnostics across independent studies, leading to the identification of a better reference test and improved confidence in prevalence estimates.

Burden of typhoid fever in low-income and middle-income countries: a systematic, literature-based update with risk-factor adjustment

BACKGROUND

No access to safe water is an important risk factor for typhoid fever, yet risk-level heterogeneity is unaccounted for in previous global burden estimates. Since WHO has recommended risk-based use of typhoid polysaccharide vaccine, we revisited the burden of typhoid fever in low-income and middle-income countries (LMICs) after adjusting for water-related risk.

METHODS

We estimated the typhoid disease burden from studies done in LMICs based on blood-culture-confirmed incidence rates applied to the 2010 population, after correcting for operational issues related to surveillance, limitations of diagnostic tests, and water-related risk. We derived incidence estimates, correction factors, and mortality estimates from systematic literature reviews. We did scenario analyses for risk factors, diagnostic sensitivity, and case fatality rates, accounting for the uncertainty in these estimates and we compared them with previous disease burden estimates.

FINDINGS

The estimated number of typhoid fever cases in LMICs in 2010 after adjusting for water-related risk was 11·9 million (95% CI 9·9-14·7) cases with 129 000 (75 000-208 000) deaths. By comparison, the estimated risk-unadjusted burden was 20·6 million (17·5-24·2) cases and 223 000 (131 000-344 000) deaths. Scenario analyses indicated that the risk-factor adjustment and updated diagnostic test correction factor derived from systematic literature reviews were the drivers of differences between the current estimate and past estimates.

INTERPRETATION

The risk-adjusted typhoid fever burden estimate was more conservative than previous estimates. However, by distinguishing the risk differences, it will allow assessment of the effect at the population level and will facilitate cost-effectiveness calculations for risk-based vaccination strategies for future typhoid conjugate vaccine.

Epidemiology, Clinical Presentation, Laboratory Diagnosis, Antimicrobial Resistance, and Antimicrobial Management of Invasive Salmonella Infections

Salmonella enterica infections are common causes of bloodstream infection in low-resource areas, where they may be difficult to distinguish from other febrile illnesses and may be associated with a high case fatality ratio. Microbiologic culture of blood or bone marrow remains the mainstay of laboratory diagnosis. Antimicrobial resistance has emerged in Salmonella enterica, initially to the traditional first-line drugs chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole. Decreased fluoroquinolone susceptibility and then fluoroquinolone resistance have developed in association with chromosomal mutations in the quinolone resistance-determining region of genes encoding DNA gyrase and topoisomerase IV and also by plasmid-mediated resistance mechanisms. Resistance to extended-spectrum cephalosporins has occurred more often in nontyphoidal than in typhoidal Salmonella strains. Azithromycin is effective for the management of uncomplicated typhoid fever and may serve as an alternative oral drug in areas where fluoroquinolone resistance is common. In 2013, CLSI lowered the ciprofloxacin susceptibility breakpoints to account for accumulating clinical, microbiologic, and pharmacokinetic-pharmacodynamic data suggesting that revision was needed for contemporary invasive Salmonella infections. Newly established CLSI guidelines for azithromycin and Salmonella enterica serovar Typhi were published in CLSI document M100 in 2015.

Diagnostics for invasive Salmonella infections: Current challenges and future directions

Invasive Salmonellosis caused by Salmonella enterica serotype Typhi or Paratyphi A, B, C, or invasive non-typhoidal Salmonella serotypes, is an immensely important disease cluster for which reliable, rapid diagnostic tests are not available. Blood culture remains the gold standard but is insensitive, slow, and resource-intensive. Existing molecular diagnostics have poor sensitivity due to the low organism burden in bodily fluids. Commercially available serologic tests for typhoidal Salmonella have had limited sensitivity and specificity. In high burden, resource-limited settings, reliance on clinical diagnosis or inaccurate tests often results in frequent, unnecessary treatment, which contributes selective pressure for the emergence of antimicrobial resistance. This practice also results in inadequate therapy for other etiologies of acute febrile illnesses, including leptospirosis and rickettsial infections. A number of novel serologic, molecular, transcriptomic and metabolomic approaches to diagnostics are under development. Target product profiles that outline specific needs may focus development and investment, and establish benchmarks for accuracy, cost, speed, and portability of new diagnostics. Of note, a critical barrier to diagnostic assay rollout will be the low cost and low perceived harm of empiric therapy on behalf of providers and patients, which leaves few perceived incentives to utilize diagnostics. Approaches that align incentives with societal goals of limiting inappropriate antimicrobial use, such as subsidizing diagnostics, may be essential for stimulating development and uptake of such assays in resource-limited settings. New diagnostics for invasive Salmonellosis should be developed and deployed alongside diagnostics for alternative etiologies of acute febrile illnesses to improve targeted use of antibiotics.

Acid exposure induces multiplication of Salmonella enterica serovar Typhi

Salmonella enterica serovar Typhi faces several environmental stresses while going through the stomach (acidic pH) to the small intestine (basic pH) and intracellularly in macrophages (acidic pH) in humans. The acidic pH followed by alkaline pH in the small intestine might be responsible for expression of certain stress-induced genes, resulting in not only better survival but also induction of multiplication and invasion of the bacterium in the small intestine. Based on this hypothesis, we developed a process wherein we exposed the blood, urine, and stool specimens from 90 acute typhoid fever patients and 36 chronic typhoid carriers to acidic pH to see the effect on isolation rate of S. Typhi. About 5 g of freshly passed unpreserved stool, a centrifuged deposit of 15 ml of urine, and 5 ml of blood clot were subjected to 5 ml of Luria-Bertani (LB) broth (pH 3.5) for 20 min, followed by enrichment in bile broth-selenite F broth. When the combined isolation from all 3 specimens, i.e., blood, urine, and stool, after acid exposure was considered, a total of 77.7% of the acute typhoid patients were observed to be positive for the isolation of the S. Typhi serotype, compared to 8.8% by the conventional method. Similarly, 42% (15/36) of chronic carriers yielded positive for S. Typhi growth after acid exposure, compared to 5.5% (2/36) by the conventional method. It therefore can be concluded that acid shock triggers the multiplication of the bacteria, resulting in better isolation rates from blood clot, stool, and urine specimens.

A comparative study of Widal test with blood culture in the diagnosis of typhoid fever in febrile patients

Background

Typhoid fever is a major health problem in developing countries and its diagnosis on clinical ground is difficult. Diagnosis in developing countries including Ethiopia is mostly done by Widal test. However, the value of the test has been debated. Hence, evaluating the result of this test is necessary for correct interpretation of the result. The main aim of this study was to compare the result of Widal test and blood culture in the diagnosis of typhoid fever in febrile patients.

Methods

Blood samples were collected from 270 febrile patients with symptoms clinically similar to typhoid fever and visiting St. Paul’s General Specialized Hospitals from mid December 2010 to March 2011. Blood culture was used to isolate S.typhi and S.paratyphi. Slide agglutination test and tube agglutination tests were used for the determination of antibody titer. An antibody titer of ≥1:80 for anti TO and ≥1:160 for anti TH were taken as a cut of value to indicate recent infection of typhoid fever.

Results

One hundred and eighty six (68.9%) participants were females and eighty four (31.1%) were males. 7 (2.6%) cases of S. typhi and 4 (1.5%) cases of S. paratyphi were identified with the total prevalence of typhoid fever 4.1%. The total number of patients who have indicative of recent infection by either of O and H antigens Widal test is 88 (32.6%). The sensitivity, specificity, Positive predictive Value and Negative predictive Value of Widal test were 71.4%, 68.44%, 5.7% and 98.9% respectively.

Conclusions

Widal test has a low sensitivity, specificity and PPV, but it has good NPV which indicates that negative Widal test result have a good indication for the absence of the disease.

A multiplex nested PCR for the simultaneous detection of Salmonella typhi, Mycobacterium tuberculosis, and Burkholderia pseudomallei in patients with pyrexia of unknown origin (PUO) in Vellore, South India

BACKGROUND AND OBJECTIVES

Salmonella typhi, Mycobacterium tuberculosis, and Burkholderia pseudomallei are among the most important monocyte-tropic bacterial agents causing pyrexia of unknown origin (PUO), with a significant number of endemic infections in both South and Southeast Asian regions. These infections pose a major risk to travelers to these regions as well.

METHODS

We developed and evaluated a multiplex nested polymerase chain reaction (PCR) for the simultaneous detection of the three pathogens in 305 patients' buffy coat samples.

RESULTS

The assay for S. typhi and B. pseudomallei was able to detect down to 1 colony forming unit/5 μL PCR input and M. tuberculosis was detected down to 20 genome copies/5 μL PCR input. S. typhi was detected in 10 (3.3 %) individuals, B. pseudomallei in 10 individuals (3.3 %), and M. tuberculosis in 18 individuals (5.9 %). Co-infections of M. tuberculosis and B. pseudomallei were detected in three individuals and S. typhi and B. pseudomallei in two individuals.

CONCLUSION

This protocol is efficient for PUO diagnosis especially in Asian countries.

Evaluation of an electricity-free, culture-based approach for detecting typhoidal Salmonella bacteremia during enteric fever in a high burden, resource-limited setting

BACKGROUND

In many rural areas at risk for enteric fever, there are few data on Salmonella enterica serotypes Typhi (S. Typhi) and Paratyphi (S. Paratyphi) incidence, due to limited laboratory capacity for microbiologic culture. Here, we describe an approach that permits recovery of the causative agents of enteric fever in such settings. This approach involves the use of an electricity-free incubator based upon use of phase-change materials. We compared this against conventional blood culture for detection of typhoidal Salmonella.

METHODOLOGY/PRINCIPAL FINDINGS

Three hundred and four patients with undifferentiated fever attending the outpatient and emergency departments of a public hospital in the Kathmandu Valley of Nepal were recruited. Conventional blood culture was compared against an electricity-free culture approach. Blood from 66 (21.7%) patients tested positive for a Gram-negative bacterium by at least one of the two methods. Sixty-five (21.4%) patients tested blood culture positive for S. Typhi (30; 9.9%) or S. Paratyphi A (35; 11.5%). From the 65 individuals with culture-confirmed enteric fever, 55 (84.6%) were identified by the conventional blood culture and 60 (92.3%) were identified by the experimental method. Median time-to-positivity was 2 days for both procedures. The experimental approach was falsely positive due to probable skin contaminants in 2 of 239 individuals (0.8%). The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% (95% CI: 80.0%-97.0%) and 96.0% (92.7%-98.1%), respectively. After initial incubation, Salmonella isolates could be readily recovered from blood culture bottles maintained at room temperature for six months.

CONCLUSIONS/SIGNIFICANCE

A simple culture approach based upon a phase-change incubator can be used to isolate agents of enteric fever. This approach could be used as a surveillance tool to assess incidence and drug resistance of the etiologic agents of enteric fever in settings without reliable local access to electricity or local diagnostic microbiology laboratories.

A novel method of selective removal of human DNA improves PCR sensitivity for detection of Salmonella Typhi in blood samples

Background

Enteric fever is a major public health problem, causing an estimated 21million new cases and 216,000 or more deaths every year. Current diagnosis of the disease is inadequate. Blood culture only identifies 45 to 70% of the cases and is time-consuming. Serological tests have very low sensitivity and specificity. Clinical samples obtained for diagnosis of enteric fever in the field generally have <1 organism/ml of blood, so that even PCR-based methods, widely used for detection of other infectious diseases, are not a straightforward option in typhoid diagnosis. We developed a novel method to enrich target bacterial DNA by selective removal of human DNA from blood samples, enhancing the sensitivity of PCR tests. This method offers the possibility of improving PCR assays directly using clinical specimens for diagnosis of this globally important infectious disease.

Methods

Blood samples were mixed with ox bile for selective lysis of human blood cells and the released human DNA was then digested with addition of bile resistant micrococcal nuclease. The intact Salmonella Typhi bacteria were collected from the specimen by centrifugation and the DNA extracted with QIAamp DNA mini kit. The presence of Salmonella Typhi bacteria in blood samples was detected by PCR with the fliC-d gene of Salmonella Typhi as the target.

Results

Micrococcal nuclease retained activity against human blood DNA in the presence of up to 9% ox bile. Background human DNA was dramatically removed from blood samples through the use of ox bile lysis and micrococcal nuclease for removal of mammalian DNA. Consequently target Salmonella Typhi DNA was enriched in DNA preparations and the PCR sensitivity for detection of Salmonella Typhi in spiked blood samples was enhanced by 1,000 fold.

Conclusions

Use of a combination of selective ox-bile blood cell lysis and removal of human DNA with micrococcal nuclease significantly improves PCR sensitivity and offers a better option for improved typhoid PCR assays directly using clinical specimens in diagnosis of this globally important infection disease which we believe could be of importance in improving clinical care and providing effective evaluation of novel vaccines.

The burden of invasive bacterial infections in Pemba, Zanzibar

Background

We conducted a surveillance study to determine the leading causes of bloodstream infection in febrile patients seeking treatment at three district hospitals in Pemba Island, Zanzibar, Tanzania, an area with low malaria transmission.

Methods

All patients above two months of age presenting to hospital with fever were screened, and blood was collected for microbiologic culture and malaria testing. Bacterial sepsis and malaria crude incidence rates were calculated for a one-year period and were adjusted for study participation and diagnostic sensitivity of blood culture.

Results

Blood culture was performed on 2,209 patients. Among them, 166 (8%) samples yielded bacterial growth; 87 (4%) were considered as likely contaminants; and 79 (4%) as pathogenic bacteria. The most frequent pathogenic bacteria isolated were Salmonella Typhi (n = 46; 58%), followed by Streptococcus pneumoniae (n = 12; 15%). The crude bacteremia rate was 6/100,000 but when adjusted for potentially missed cases the rate may be as high as 163/100,000. Crude and adjusted rates for S. Typhi infections and malaria were 4 and 110/100,000 and 4 and 47/100,000, respectively. Twenty three (51%), 22 (49%) and 22 (49%) of the S.Typhi isolates were found to be resistant toward ampicillin, chloramphenicol and cotrimoxazole, respectively. Multidrug resistance (MDR) against the three antimicrobials was detected in 42% of the isolates.

Conclusions

In the presence of very low malaria incidence we found high rates of S. Typhi and S. pneumoniae infections on Pemba Island, Zanzibar. Preventive measures such as vaccination could reduce the febrile disease burden.

Prevalence of Salmonella typhi among patients with febrile illness in rural and peri-urban populations of Vellore district, as determined by nested PCR targeting the flagellin gene

BACKGROUND AND OBJECTIVE

Fever is one of the most common illnesses in all age groups in India. Typhoid fever is a continuing problem in developing countries such as India, which has poor sanitation facilities. The diagnosis of typhoid fever is still made by conventional culture-based isolation and identification. Serologic diagnostic tests, though widely used, have many deficiencies. Our objective was to investigate a molecular nested polymerase chain reaction (nPCR) technique to detect Salmonella typhi among patients with febrile illness in rural and peri-urban communities in Vellore district (Tamil Nadu, India).

METHODS

nPCR targeting the flagellin gene (fliC) was carried out using HotStar Taq DNA polymerase on DNA extracted from the buffy coat fraction of blood samples. Blood culture was done in a completely automated blood culture system, BacT/Alert(R), on prospectively collected blood samples. Relevant clinicopathologic data were obtained.

RESULTS

nPCR was found to have a lower limit of detection of 0.01 colony-forming units per milliliter. The prevalence of typhoid fever as estimated by nPCR was 4.7% in pyrexia of unknown origin (PUO) in the rural/peri-urban communities of Vellore district. The prevalence of S. typhi as estimated by blood culture was 2.0%, which was lower than the nPCR estimation. nPCR had sensitivity and specificity of 100% and 97.3%, respectively. The observed agreement between blood culture and nPCR was 0.973 and the Kappa coefficient was 0.59 (p < 0.0001). The frequency of typhoid fever as detected by nPCR was 4.35% among rural patients and 5.32% among peri-urban individuals.

CONCLUSION

nPCR on DNA extracts of buffy-coat samples using HotStar Taq was found to be a valuable and specific technique for diagnosis of typhoid fever.

A fast and highly sensitive blood culture PCR method for clinical detection of Salmonella enterica serovar Typhi

Background

Salmonella Typhi causes an estimated 21 million new cases of typhoid fever and 216,000 deaths every year. Blood culture is currently the gold standard for diagnosis of typhoid fever, but it is time-consuming and takes several days for isolation and identification of causative organisms. It is then too late to initiate proper antibiotic therapy. Serological tests have very low sensitivity and specificity, and no practical value in endemic areas. As early diagnosis of the disease and prompt treatment are essential for optimal management, especially in children, a rapid sensitive detection method for typhoid fever is urgently needed. Although PCR is sensitive and rapid, initial research indicated similar sensitivity to blood culture and lower specificity. We developed a fast and highly sensitive blood culture PCR method for detection of Salmonella Typhi, allowing same-day initiation of treatment after accurate diagnosis of typhoid.

Methods

An ox bile tryptone soy broth was optimized for blood culture, which allows the complete lysis of blood cells to release intracellular bacteria without inhibiting the growth of Salmonella Typhi. Using the optimised broth Salmonella Typhi bacteria in artificial blood samples were enriched in blood culture and then detected by a PCR targeting the fliC-d gene of Salmonella Typhi.

Results

Tests demonstrated that 2.4% ox bile in blood culture not only lyzes blood cells completely within 1.5 hours so that the intracellular bacteria could be released, but also has no inhibiting effect on the growth of Salmonella Typhi.

Three hour enrichment of Salmonella Typhi in tryptone soya broth containing 2.4% ox bile could increase the bacterial number from 0.75 CFU per millilitre of blood which is similar to clinical typhoid samples to the level which regular PCR can detect. The whole blood culture PCR assay takes less than 8 hours to complete rather than several days for conventional blood culture.

Conclusions

This novel blood culture PCR method is superior in speed and sensitivity to both conventional blood culture and PCR assays. Its use in clinical diagnosis may allow early detection of the causative organism and facilitate initiation of prompt treatment among patients with typhoid fever.