Enteric fever in Cambodian children is dominated by multidrug-resistant H58 Salmonella enterica serovar Typhi with intermediate susceptibility to ciprofloxacin

Prevalence of Salmonella spp. in meat, seafood, and leafy green vegetables from local markets and vegetable farms in Phnom Penh, Cambodia

Salmonella is a major bacterial concern for public health globally. Although there are limited documentation on the prevalence of Salmonella species in Cambodia's food chain, some reports indicate that salmonellosis is a severe gastrointestinal infection in its population and especially in children. To investigate the presence of Salmonella spp., 285 food samples (75 meat, 50 seafood, and 160 leafy green vegetable samples) were randomly collected from various local markets in Phnom Penh capital and nearby farms in Cambodia. Concurrently, field observations were conducted to collect data on food hygiene and practices among the relevant actors. All food samples were analyzed using bacterial culture and plate counts, and the findings were confirmed serially with biochemical, serological, and PCR tests. The observational data on food hygiene and practices from farm to market revealed that the spread of Salmonella in the food-value chain from farm to market could pose health risks to consumers. The overall prevalence of Salmonella spp. was 48.4% (138/285), while the prevalence in meat, seafood, and vegetables was 71% (53/75), 64% (32/50), and 33% (53/160), respectively. Mean Salmonella plate count ranged from 1.2 to 7.40 log10 CFU/g, and there was no significant difference in bacterial counts between meat, seafood, and vegetable samples (p > 0.05). The most common serogroups among the isolated Salmonella spp. were B and C. These results suggest that a large proportion of meat, seafood, and vegetable products sold at local markets in Phnom Penh are contaminated with Salmonella spp. This is likely linked to inadequate hygiene and sanitation practices, including handling, storage, and preservation conditions. Observations on farms suggested that the prevalence of Salmonella in vegetables sold at the market could be linked to contamination relating to agricultural practices. Thus, controlling the spread of foodborne salmonellosis through the food-value chain from farms and retailers to consumers is warranted to enhance food safety in Cambodia.

Salmonella Bloodstream Infections

Salmonella is a major foodborne pathogen of both animals and humans. This bacterium is responsible for considerable morbidity and mortality world-wide. Different serovars of this genus cause diseases ranging from self-limiting gastroenteritis to a potentially fatal systemic disease known as enteric fever. Gastrointestinal infections with Salmonella are usually self-limiting and rarely require medical intervention. Bloodstream infections, on the other hand, are often fatal even with hospitalization. This review describes the routes and underlying mechanisms of the extraintestinal dissemination of Salmonella and the chronic infections that sometimes result. It includes information on the pathogenicity islands and individual virulence factors involved in systemic dissemination as well as a discussion of the host factors that mediate susceptibility. Also, the major outbreaks of invasive Salmonella disease in the tropics are described.

Quantitative risk assessment of salmonellosis in Cambodian consumers through chicken and pork salad consumption

Salmonella is a globally important foodborne bacterial pathogen that poses a high risk to human health. This study aimed to estimate the risk to Cambodian consumers from acquiring salmonellosis after consuming chicken and pork salad, using a quantitative microbial risk assessment (QMRA). Chicken and pork salads are typical Cambodian dishes containing raw vegetables and boiled chicken meat or pork. As previously described, chicken meat and pork samples (n = 204 of each) were collected from traditional markets in 25 Cambodian provinces to generate data on Salmonella contamination. Salad preparation and consumption practices were surveyed in 93 Cambodian households and this information was used to design an experiment to assess Salmonella cross-contamination from raw meat to ready-to-eat salad. In the part of the study reported here, data on consumption, Salmonella in salad, dose-response, and predicted salmonellosis were modeled using Monte Carlo simulations at 10,000 iterations. The prevalence of Salmonella in chicken meat and pork were set to 42.6 and 45.1%, respectively, with average most probable number (MPN) per gram of Salmonella in chicken meat was 10.6 and in pork 11.1 MPN/g, based on an earlier study. Half of the interviewed households cooked meat for the salad directly after purchase. The QMRA model showed that the modeled annual risk of salmonellosis from consuming chicken salad, pork salad and both chicken and pork salad were 11.1% probability of illness per person per year (90% CI 0.0–35.1), 4.0% (90% CI 0.0–21.3), and 14.5% (90% CI 0.0–33.5), respectively. The factors most influencing the estimate were cross-contamination while preparing the salad, followed by the prevalence of Salmonella in chicken meat and pork at the market. The wide confidence interval for the incidence was mainly due to the variability in reducing bacteria concentration by cooking and salad consumption. The predicted risk of salmonellosis due to chicken and pork salad consumption is high, and the study provides evidence supporting control measures of improving the safety of retailed chicken and pork obtained from markets to households and improving food preparation methods in the household.

Complications and mortality of non-typhoidal salmonella invasive disease: a global systematic review and meta-analysis

BACKGROUND

Non-typhoidal salmonella can cause serious, life-threatening invasive infections involving the bloodstream and other normally sterile sites. We aimed to systematically review the prevalence of complications and case-fatality ratio (CFR) of non-typhoidal salmonella invasive disease to provide contemporary global estimates and inform the development of vaccine and non-vaccine interventions.

METHODS

We did a global systematic review and meta-analysis of studies investigating the complications and mortality associated with non-typhoidal salmonella invasive disease. We searched Embase, MEDLINE, Web of Science, and PubMed for peer-reviewed, primary research articles published from database inception up to June 4, 2021, with no restrictions on language, country, date, or participant demographics. Only studies reporting the proportion of complications or deaths associated with non-typhoidal salmonella invasive disease, confirmed by culture of samples taken from a normally sterile site (eg, blood or bone marrow) were included. We excluded case reports, case series, policy reports, commentaries, editorials, and conference abstracts. Data on the prevalence of complications and CFR were abstracted. The primary outcomes were to estimate the prevalence of complications and CFR of non-typhoidal salmonella invasive disease. We calculated an overall pooled CFR estimate and pooled CFR stratified by UN region, subregion, age group, and by serovar when available with a random-effects meta-analysis. A risk-of-bias assessment was done, and heterogeneity was assessed with Cochran's Q Test, I2, and τ2. This study was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, and is registered with PROSPERO, CRD42020202293.

FINDINGS

The systematic review returned a total of 8770 records. After duplicates were removed, 5837 titles and abstracts were screened, yielding 84 studies from 35 countries after exclusions. Of these included studies, 77 (91·7%) were hospital-based and 66 (78·6%) were located in Africa or Asia. Among 55 studies reporting non-typhoidal salmonella disease-associated complications, a total of 45 different complications were reported and 1824 complication events were identified among 6974 study participants. The most prevalent complication was septicaemia, occurring in 171 (57·2%) of 299 participants, followed by anaemia in 580 (47·3%) of 1225 participants. From 81 studies reporting the CFR of non-typhoidal salmonella invasive disease, the overall pooled CFR estimate was 14·7% (95% CI 12·2-17·3). When stratified by UN region, the pooled CFR was 17·1% (13·6-21·0) in Africa, 14·0% (9·4-19·4) in Asia, 9·9% (6·4-14·0) in Europe, and 9·6% (0·0-25·1) in the Americas. Of all 84 studies, 66 (78·6%) had an overall high risk of bias, 18 (21·4%) had a moderate risk, and none had a low risk. Substantial heterogeneity (I2>80%) was observed in most (15 [65·2%] of 23) CFR estimates.

INTERPRETATION

Complications were frequent among individuals with non-typhoidal salmonella invasive disease and approximately 15% of patients died. Clinicians, especially in African countries, should be aware of non-typhoidal salmonella invasive disease as a cause of severe febrile illness. Prompt diagnoses and management decisions, including empiric antimicrobial therapy, would improve patient outcomes. Additionally, investments in improving clinical microbiology facilities to identify non-typhoidal salmonella and research efforts towards vaccine development and non-vaccine prevention measures would prevent non-typhoidal salmonella invasive disease-associated illness and death.

FUNDING

EU Horizon 2020 research and innovation programme.

Antimicrobial resistance detection in Southeast Asian hospitals is critically important from both patient and societal perspectives, but what is its cost?

Antimicrobial resistance (AMR) is a major threat to global health. Improving laboratory capacity for AMR detection is critically important for patient health outcomes and population level surveillance. We aimed to estimate the financial cost of setting up and running a microbiology laboratory for organism identification and antimicrobial susceptibility testing as part of an AMR surveillance programme. Financial costs for setting up and running a microbiology laboratory were estimated using a top-down approach based on resource and cost data obtained from three clinical laboratories in the Mahidol Oxford Tropical Medicine Research Unit network. Costs were calculated for twelve scenarios, considering three levels of automation, with equipment sourced from either of the two leading manufacturers, and at low and high specimen throughput. To inform the costs of detection of AMR in existing labs, the unit cost per specimen and per isolate were also calculated using a micro-costing approach. Establishing a laboratory with the capacity to process 10,000 specimens per year ranged from $254,000 to $660,000 while the cost for a laboratory processing 100,000 specimens ranged from $394,000 to $887,000. Excluding capital costs to set up the laboratory, the cost per specimen ranged from $22-31 (10,000 specimens) and $11-12 (100,000 specimens). The cost per isolate ranged from $215-304 (10,000 specimens) and $105-122 (100,000 specimens). This study provides a conservative estimate of the costs for setting up and running a microbiology laboratory for AMR surveillance from a healthcare provider perspective. In the absence of donor support, these costs may be prohibitive in many low- and middle- income country (LMIC) settings. With the increased focus on AMR detection and surveillance, the high laboratory costs highlight the need for more focus on developing cheaper and cost-effective equipment and reagents so that laboratories in LMICs have the potential to improve laboratory capacity and participate in AMR surveillance.

Antimicrobial Resistance in endemic enteric infections in Kenya and the region, and efforts towards addressing the challenges

Resistance to commonly available antimicrobials is a major threat to the fight against endemic bacterial diseases in sub-Saharan Africa, with a majority of the population unable to afford alternative effective antimicrobial options for management of these diseases. Diseases such as typhoid, cholera, and invasive nontyphoidal Salmonella are among the key enteric infections endemic in most parts of sub-Saharan Africa, especially in displaced populations and among the urban populations living in overcrowded informal settlements. Here, we explore the prevalence and the genomic epidemiology of these infections and the growing problem of multidrug resistance, including emerging resistance to the last line of treatment for these infections. Prevalence rates to commonly available antimicrobials, including ampicillin, chloramphenicol, cotrimoxazole, and tetracycline, now range between 65% and 80%, while 15%–20% of recently studied isolates show reduced susceptibility to fluoroquinolones and emerging resistance to extended-spectrum β-lactams mediated by the CTX-M-15 gene carried on a highly mobile genetic element. The high prevalence of multidrug-resistant isolates including resistance to reserve antibiotics, calls for enhanced control and management options. It will be important for governments in the region to enhance the implementation of national action plans, as guided by the global action plan championed by the World Health Organization, to combat the threat of antimicrobial resistance. However, to yield meaningful results, these efforts will require a strong commitment and enhancement at all levels of healthcare in order. In addition, the use of World Health Organization–approved vaccines in the short to medium term and improvement of water and sanitation in the long term will reduce the burden of disease and antimicrobial resistance in the region.

Bactericidal activities and post-antibiotic effects of ofloxacin and ceftriaxone against drug-resistant Salmonella enterica serovar Typhi

BACKGROUND

The clinical response to ceftriaxone in patients with typhoid fever is significantly slower than with ofloxacin, despite infection with Salmonella enterica serovar Typhi (S. Typhi) isolates with similar susceptibilities (MIC 0.03-0.12 mg/L). The response to ofloxacin is slower if the isolate has intermediate susceptibility (MIC 0.25-1.0 mg/L).

OBJECTIVES

To determine the bactericidal activity and post-antibiotic effect (PAE) of ceftriaxone and ofloxacin against S. Typhi.

METHODS

The mean time to reach a 99.9% reduction in log10 count (bactericidal activity) and PAE of ceftriaxone and ofloxacin were determined for 18 clinical isolates of S. Typhi in time-kill experiments (MIC range for ofloxacin 0.06-1.0 mg/L and for ceftriaxone 0.03-0.12 mg/L).

RESULTS

The mean (SD) bactericidal activity of ofloxacin was 33.1 (15.2) min and 384.4 (60) min for ceftriaxone. After a 30 min exposure to ofloxacin, the mean (SD) duration of PAE was 154.7 (52.6) min. There was no detectable PAE after 1 h of exposure to ceftriaxone. For ofloxacin, bactericidal activity and PAE did not significantly differ between isolates with full or intermediate susceptibility provided ofloxacin concentrations were maintained at 4×MIC.

CONCLUSIONS

Infections with S. Typhi with intermediate ofloxacin susceptibility may respond to doses that maintain ofloxacin concentrations at 4×MIC at the site of infection. The slow bactericidal activity of ceftriaxone and absent PAE may explain the slow clinical response in typhoid.

Phylogenetic Analysis Indicates a Longer Term Presence of the Globally Distributed H58 Haplotype of Salmonella Typhi in Southern India

Background

Typhoid fever caused by Salmonella Typhi is a major public health concern in low-/middle-income countries. A recent study of 1900 global S. Typhi indicated that South Asia might be the site of the original emergence of the most successful and hypervirulent clone belonging to the 4.3.1 genotype. However, this study had limited samples from India.

Methods

We analyzed 194 clinical S. Typhi, temporal representatives from those isolated from blood and bone marrow cultures in southern India, over 26 years (1991–2016). Antimicrobial resistance (AMR) testing was performed for most common clinical agents. Whole-genome sequencing and SNP-level analysis was conducted. Comparative genomics of Vellore isolates was performed to infer transmission and AMR events.

Results

We identified multidrug-resistance (MDR)–associated clade 4.3.1 as the dominant genotype. We detected 4.3.1 S. Typhi as early as 1991, the earliest to be reported form India, and the majority were fluoroquinolone resistant and not MDR. MDR was not detected at all in other genotypes circulating in Vellore. Comparison with global S. Typhi showed 2 Vellore subgroups (I and II) that were phylogenetically highly related to previously described South Asia (subgroup I, II) and Southeast Asia (subgroup II) clades.

Conclusions

4.3.1 S. Typhi has dominated in Vellore for 2 decades. Our study would assist public health agencies in better tracking of transmission and persistence of this successful clade in India and globally. It informs clinicians of the AMR pattern of circulating clone, which would add confidence to their prophylactic/treatment decision making and facilitate efficient patient care.

Typhoid in Laos: An 18-Year Perspective

Although typhoid is endemic to Southeast Asia, very little is known about the disease in Laos. Typhoid vaccination is not included in the national immunization program. Although sanitation has improved, one million people still do not have access to basic clean water sources. We describe the epidemiology and antimicrobial susceptibility patterns of Salmonella enterica serovar Typhi (S. Typhi) infection in Laos based on isolates accrued over 18 years at Mahosot Hospital, Vientiane. All blood cultures collected from patients presenting with fever submitted to the Microbiology Laboratory at Mahosot Hospital (February 2000–December 2018) were included. This included patients from Vientiane and four provincial hospitals and one typhoid outbreak investigation. A total of 913 (1.5%) of 60,384 blood cultures were positive for S. Typhi. The majority of isolates with data available (712/898, 79.3%) were susceptible to all antibiotics tested, with 59 (6.5%) multidrug-resistant (MDR) isolates, mostly from one outbreak. Of 854 isolates, 12 (1.4%) were fluoroquinolone resistant. Patient admissions peaked between March and June at the end of the dry season. Although there are key limitations, these data give the first detailed epidemiological evidence of typhoid in Laos. However, estimates will be greatly influenced by access to blood culture services and health-seeking behavior. Although typhoid multidrug resistance and fluoroquinolone resistance are not currently major issues in Laos, continued surveillance and improved antibiotic stewardship are necessary to forestall worsening of the situation. Cost-effectiveness analysis is needed to inform decisions regarding typhoid vaccine introduction.

Salmonella Typhi and Paratyphi A infections in Cambodian children, 2012-2016

OBJECTIVES

Enteric fever remains an important diagnostic and treatment challenge in febrile children living in the tropics. In the context of a national Salmonella enterica serovar Paratyphi A outbreak, the objective of this retrospective study was to compare features of S. Typhi and S. Paratyphi A infections in Cambodian children.

METHODS

Clinical and laboratory features were reviewed for 192 blood culture-confirmed children with S. Typhi and S. Paratyphi A infections presenting to a paediatric referral hospital in Siem Reap, 2012-2016.

RESULTS

Children with S. Typhi infections were younger, were more likely to have chills and/or diarrhoea, and were more frequently hospitalized than those with S. Paratyphi A infections. Over three quarters (88.3%) of S. Typhi isolates were multidrug-resistant, compared to none of the S. Paratyphi A.

CONCLUSIONS

In this small study of Cambodian children, S. Typhi infections were more severe than S. Paratyphi A infections. Antibiotic resistance limits treatment options for enteric fever in this population.

Factors associated with occurrence of salmonellosis among children living in Mukuru slum, an urban informal settlement in Kenya

Background

In Kenya, typhoid fever and invasive non-typhoidal salmonellosis present a huge burden of disease, especially in poor-resource settings where clean water supply and sanitation conditions are inadequate. The epidemiology of both diseases is poorly understood in terms of severity and risk factors. The aim of the study was to determine the disease burden and spatial distribution of salmonellosis, as well as socioeconomic and environmental risk factors for these infections, in a large informal settlement near the city of Nairobi, from 2013 to 2017.

Methods

Initially, a house-to-house baseline census of 150,000 population in Mukuru informal settlement was carried out and relevant socioeconomic, demographic, and healthcare utilization information was collected using structured questionnaires. Salmonella bacteria were cultured from the blood and faeces of children < 16 years of age who reported at three outpatient facilities with fever alone or fever and diarrhea. Tests of association between specific Salmonella serotypes and risk factors were conducted using Pearson Chi-Square (χ²) test.

Results

A total of 16,236 children were recruited into the study. The prevalence of bloodstream infections by Non-Typhoidal Salmonella (NTS), consisting of Salmonella Typhimurium/ Enteriditis, was 1.3%; Salmonella Typhi was 1.4%, and this was highest among children < 16 years of age. Occurrence of Salmonella Typhimurium/ Enteriditis was not significantly associated with rearing any domestic animals. Rearing chicken was significantly associated with high prevalence of S. Typhi (2.1%; p = 0.011). The proportion of children infected with Salmonella Typhimurium/ Enteriditis was significantly higher in households that used water pots as water storage containers compared to using water directly from the tap (0.6%). Use of pit latrines and open defecation were significant risk factors for S. Typhi infection (1.6%; p = 0.048). The proportion of Salmonella Typhimurium/ Enteriditis among children eating street food 4 or more times per week was higher compared to 1 to 2 times/week on average (1.1%; p = 0.032).

Conclusion

Typhoidal and NTS are important causes of illness in children in Mukuru informal settlement, especially among children less than 16 years of age. Improving Water, Sanitation and Hygiene (WASH) including boiling water, breastfeeding, hand washing practices, and avoiding animal contact in domestic settings could contribute to reducing the risk of transmission of Salmonella disease from contaminated environments.

Enteric Fever in Cambodia: Community Perceptions and Practices Concerning Disease Transmission and Treatment

Enteric fever is a systemic bacterial infection in humans that is endemic in Cambodia and for which antibiotic resistance is increasingly reported. To guide public health programs, this qualitative study sought to explore community perceptions on transmission and treatment. Participant observation was carried out in hospital settings, pharmacies, and at a community level in Phnom Penh. In-depth interviews 39 and one focus group discussion were carried out with blood culture–confirmed enteric fever patients and purposively selected key informants. Informants were theoretically sampled based on initial themes identified using abductive analysis. Nvivo 11 was used for thematic coding. An urgent need to address health literacy concerning the transmission of enteric fever was identified, as lay informants did not link the disease and its symptoms to bacterial contamination of foods and drinks but rather to foods considered “bad” following humoral illness interpretations. As a result, lay informants considered recurrence of enteric fever preventable with appropriate dietary restrictions and Khmer traditional medicines. This study also reveals pluralistic health-care–seeking behavior. For initial and mild symptoms, patients preferred home treatment or traditional healing practices; limited household finances delayed treatment seeking. When symptoms persisted, patients first visited drug outlets or private practitioners, where they received a mix of nonessential medicines and one or more antibiotics often without prescription or confirmation of diagnosis. Inappropriate use of antibiotics was common and was related to diagnostic uncertainty and limited finances, factors which should be addressed during future efforts to improve the uptake of appropriate diagnostics and treatment of enteric fever.

Antimicrobial resistance in Cambodia: a review

OBJECTIVES

Following the launch of the Global Antimicrobial Resistance Surveillance System (GLASS), antimicrobial resistance (AMR) rates in many countries remain poorly described. This review provides an overview of published AMR data from Cambodia in the context of recently initiated national human and food-animal surveillance.

METHODS

PubMed and the Cochrane Database of Systematic Reviews were searched for articles published from 2000 to 2018, which reported antimicrobial susceptibility testing (AST) data for GLASS specific organisms isolated from Cambodia. Articles were screened using strict inclusion/exclusion criteria. AST data was extracted, with medians and ranges of resistance rates calculated for specific bug-drug combinations.

RESULTS

Twenty-four papers were included for final analysis, with 20 describing isolates from human populations. Escherichia coli was the most commonly described organism, with median resistance rates from human isolates of 92.8% (n=6 articles), 46.4% (n=4), 55.4% (n=8), and 46.4% (n=5) to ampicillin, 3^rd generation cephalosporins, fluoroquinolones, and gentamicin respectively.

CONCLUSIONS

Whilst resistance rates are high for several GLASS organisms, there were insufficient data to draw robust conclusions about the AMR situation in Cambodia. The recently implemented national AMR surveillance systems will begin to address this data gap.

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa.

Typhoid fever is caused by the bacterium Salmonella Typhi. Here, Park et al. analyse the genomes of 249 S. Typhi isolates from 11 sub-Saharan African countries, identifying genes and plasmids associated with antibiotic resistance and showing that multi-drug resistance is highly pervasive in sub-Saharan Africa.

Modelling the cost-effectiveness of a rapid diagnostic test (IgMFA) for uncomplicated typhoid fever in Cambodia

Typhoid fever is a common cause of fever in Cambodian children but diagnosis and treatment are usually presumptive owing to the lack of quick and accurate tests at an initial consultation. This study aimed to evaluate the cost-effectiveness of using a rapid diagnostic test (RDT) for typhoid fever diagnosis, an immunoglobulin M lateral flow assay (IgMFA), in a remote health centre setting in Cambodia from a healthcare provider perspective. A cost-effectiveness analysis (CEA) with decision analytic modelling was conducted. We constructed a decision tree model comparing the IgMFA versus clinical diagnosis in a hypothetical cohort with 1000 children in each arm. The costs included direct medical costs only. The eligibility was children (≤14 years old) with fever. Time horizon was day seven from the initial consultation. The number of treatment success in typhoid fever cases was the primary health outcome. The number of correctly diagnosed typhoid fever cases (true-positives) was the intermediate health outcome. We obtained the incremental cost effectiveness ratio (ICER), expressed as the difference in costs divided by the difference in the number of treatment success between the two arms. Sensitivity analyses were conducted. The IgMFA detected 5.87 more true-positives than the clinical diagnosis (38.45 versus 32.59) per 1000 children and there were 3.61 more treatment successes (46.78 versus 43.17). The incremental cost of the IgMFA was estimated at $5700; therefore, the ICER to have one additional treatment success was estimated to be $1579. The key drivers for the ICER were the relative sensitivity of IgMFA versus clinical diagnosis, the cost of IgMFA, and the prevalence of typhoid fever or multi-drug resistant strains. The IgMFA was more costly but more effective than the clinical diagnosis in the base-case analysis. An IgMFA could be more cost-effective than the base-case if the sensitivity of IgMFA was higher or cost lower. Decision makers may use a willingness-to-pay threshold that considers the additional cost of hospitalisation for treatment failures.

Why Is Eradicating Typhoid Fever So Challenging: Implications for Vaccine and Therapeutic Design

Salmonella enterica serovar Typhi (S. Typhi) and S. Paratyphi, namely typhoidal Salmonellae, are the cause of (para) typhoid fever, which is a devastating systemic infectious disease in humans. In addition, the spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) S. Typhi in many low and middle-income countries poses a significant risk to human health. While currently available typhoid vaccines and therapeutics are efficacious, they have some limitations. One important limitation is the lack of controlling individuals who chronically carry S. Typhi. However, due to the strict host specificity of S. Typhi to humans, S. Typhi research is hampered. As a result, our understanding of S. Typhi pathogenesis is incomplete, thereby delaying the development and improvement of prevention and treatment strategies. Nonetheless, to better combat and contain S. Typhi, it is vital to develop a vaccine and therapy for controlling both acutely and chronically infected individuals. This review discusses how scientists are trying to combat typhoid fever, why it is so challenging to do so, which approaches show promise, and what we know about the pathogenesis of S. Typhi chronic infection.

Pervasive antibiotic misuse in the Cambodian community: antibiotic-seeking behaviour with unrestricted access

Background

Antibiotic misuse is widespread in resource-limited countries such as Cambodia where the burden of infectious diseases is high and access to antibiotics is unrestricted. We explored healthcare seeking behaviour related to obtaining antibiotics and drivers of antibiotic misuse in the Cambodian community.

Methods

In-depth interviews were held with family members of patients being admitted in hospitals and private pharmacies termed pharmacy attendants in the catchment areas of the hospitals. Nurses who run community primary healthcare centres located within the hospital catchment areas were invited to attend focus group discussions. Nvivo version 10 was used to code and manage thematic data analysis.

Results

We conducted individual interviews with 35 family members, 7 untrained pharmacy attendants and 3 trained pharmacists and 6 focus group discussions with 30 nurses. Self-medication with a drug-cocktail was widespread and included broad-spectrum antibiotics for mild illness. Unrestricted access to antibiotics was facilitated by various community enablers including pharmacies or drug outlets, nurse suppliers and unofficial village medical providers referred to as “village Pett” whose healthcare training has historically been in the field and not at university. These enablers supplied the community with various types of antibiotics including broad spectrum fluoroquinolones and cephalosporins. When treatment was perceived to be ineffective patients would prescriber-shop various suppliers who would unfailingly provide them with antibiotics. The main driver of the community’s demand for antibiotics was a mistaken belief in the benefits of antibiotics for a common cold, high temperature, pain, malaria and ‘Roleak’ which includes a broad catch-all for perceived inflammatory conditions. For severe illnesses, patients would attend a community healthcare centre, hospital, or when their finances permitted, a private prescriber.

Conclusions

Pervasive antibiotic misuse was driven by a habitual supplier-seeking behaviour that was enabled by unrestricted access and misconceptions about antibiotics for mild illnesses. Unofficial suppliers must be stopped by supporting existing regulations with tough new laws aimed at outlawing supplies outside registered pharmacies and fining registered pharmacist/owners of these pharmacies for supplying antibiotics without a prescription. Community primary healthcare centres must be strengthened to become the frontline antibiotic prescribers in the community thereby enabling the community’s access to inexpensive and appropriate healthcare. Community-based education program should target appropriate health-seeking pathways and the serious consequences of antibiotic misuse.

"If it's a broad spectrum, it can shoot better": inappropriate antibiotic prescribing in Cambodia

Background

Cambodia is affected by antibiotic resistance but interventions to reduce the level of resistance require knowledge of the phenomena that lead to inappropriate prescribing. We interviewed physicians working in public hospitals to explore the drivers of inappropriate antibiotic prescribing.

Methods

Hospitals participating in a knowledge, attitudes and practices survey prior to this study were purposively selected and physicians were randomly recruited to participate in focus group discussions. Nvivo version 10 was used to inductively code the qualitative transcripts and manage thematic data analysis.

Results

Inappropriate antibiotic prescribing was a common practice and driven by seven factors: prescribing habit, limited diagnostic capacity, lack of microbiology evidence, non-evidence-based clinical guidelines, perceived patient demand, poor hygiene and infection control, and perceived bacterial resistance to narrow spectrum antibiotics.

“Every day, doctors are not performing appropriately. We have made lots of mistakes with our antibiotic prescribing.”

When a patient’s clinical condition was not responsive to empiric treatment, physicians changed to a broader spectrum antibiotic and microbiology services were sought only after failure of a treatment with a broad-spectrum antibiotic. This habitual empirical prescribing was a common practice regardless of microbiology service accessibility. Poor hygiene and infection control practices were commonly described as reasons for ‘preventive’ prescribing with full course of antibiotics while perception of bacterial resistance to narrow-spectrum antibiotics due to unrestricted access in the community resulted in unnecessary prescribing of broad spectrum antibiotics in private practices.

Conclusions

The practice of prescribing antibiotics by Cambodian physicians is inappropriate and based on prescribing habit rather than microbiology evidence. Improvement in prescribing practice is unlikely to occur unless an education program for physicians focuses on the diagnostic capacity and usefulness of microbiology services. In parallel, hygiene and infection control in hospital must be improved, evidence-based antibiotic prescribing guidelines must be developed, and access to antibiotics in community must be restricted.

Antimicrobial resistance and molecular subtypes of Salmonella enterica serovar Typhi isolates from Kolkata, India over a 15 years period 1998-2012

Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains an unresolved public health problem in India. Emergence of antimicrobial resistant strains poses a great concern for typhoid treatment and influences reshaping of current S. Typhi population. We included representative S. Typhi strains (n=164) from retrospective studies, both community and hospital based, conducted at National Institute of Cholera and Enteric Diseases, Kolkata during 15 years period (1998-2012) to analyze their antimicrobial resistance (AMR) profiles, mechanism of AMR and molecular subtypes of the strains. More than 60% of the S. Typhi isolates were obtained from community based studies. During the study period, steady decline (46.4%-15.6%) in isolation of multidrug-resistant (MDR, resistant to ampicillin, chloramphenicol and co-trimoxazole) S. Typhi was noticed with parallel increase of nalidixic acid-resistant (NAL^R) strains (60.7%-93.8%) and ciprofloxacin resistant (CIP^R) strains (0%-25%). Of 53 MDR strains, 46 (86.8%) were NAL^R showing decreased ciprofloxacin susceptible (DCS) (MIC for ciprofloxacin 0.12-0.5μg/ml) phenotype. Conjugative IncHI1 (230kb) and non-conjugative non-IncHI1 (180kb) plasmids were found in 23 (43.4%) and 14 (26.4%) MDR strains respectively, plasmid was absent in 16 (30.2%) MDR strains. MDR strains with or without plasmid shared the same set of resistance genes (bla_TEM-1, catA1, sul1, sul2, strA and strB) and class 1 integron possessing dfrA7 gene cassette. Two S. Typhi strains harbored 50kb transferrable plasmids carrying dfrA15 and aadA1 gene cassettes in class 1 integron. The majority of the strains (135/164, 82.3%) belonged to H58 haplotype. Among the MDR isolates, fluoroquinolone resistant or combined resistant isolates (n=147), 127 (86.4%) were H58 and 20 (13.6%) belonged to non-H58. NAL^RS. Typhi strains with decreased susceptibility or resistance to ciprofloxacin had point mutation(s) in quinolone resistance-determining region of gyrA and parC genes. Pulsed-field gel electrophoresis showed more diversity among NAL^RS. Typhi than MDR strains. Results of this study generated information useful for better understanding of the disease epidemiology and its control in endemic settings.

Antibiotics: practice and opinions of Cambodian commercial farmers, animal feed retailers and veterinarians

BACKGROUND

Cambodia has reported multidrug resistant bacteria in poultry, similar to other countries in the region. We visited commercial food animal farms to explore opinions and antibiotic practices on the farms.

METHODS

We used individual in-depth qualitative interviews with 16 commercial farmers, four feed retailers and nine veterinarians from food animal industry and government offices from the southwestern region of Phnom Penh. Transcribed interviews were thematically analysed.

RESULTS

Widespread antibiotic use occurred on all farms and was driven by four facilitators: belief that antibiotics were necessary for animal raising, limited knowledge, unrestricted antibiotic access, and weak monitoring and control systems. "If we treat ducks for two days and they aren't cured we change to human drugs. We cocktail 10 tablets of this, 10 tablets of that and 20 tablets of this one. Altogether 200 tablets are mixed in 100 or 200 L of water for the ducks to drink. No one taught me, just my experiences." Antibiotics were believed to be necessary for disease prevention. "On the first day when we bring in the chicks, we let them drink Enro [enrofloxacin] and vitamins to make them resist to the weather. We place them in the house and there are some bacteria in the environment. When they are newly arrived, we have to give them feed. So we're afraid they get diarrhea when they eat feed, we have to use Enro." All farmers used pre-mixed feed that veterinarians and feed retailers acknowledged contained antibiotics but not all listed the antibiotics. Farmers viewed pre-mixed feed as a necessary 'feed supplement' for growth promotion. "….The fatten supplement is mixed in feed. Pigs aren't growing well unless I use the supplement." Farmers and veterinarians were concerned that 'antibiotic residuals' in animal meat could harm human health. But they did not link this with antibiotic resistance.

CONCLUSIONS

Antibiotic use in food animals was widespread and uncontrolled. Farmers focused on the benefits of food animal production rather than concerns about the consequences of antibiotic use. Therefore, education for prudent use of antibiotics in food animals and regulations are urgently needed in food animal farming in Cambodia.

Antibiotic prescribing practices: A national survey of Cambodian physicians

BACKGROUND

Antibiotic resistance is a threat to global health security. We assessed knowledge, attitudes, and practices in regard to antibiotic prescribing and resistance in Cambodian physicians from public hospitals.

METHODS

A cross-sectional knowledge, attitudes, and practices survey was distributed to physicians from 19 public hospitals.

RESULTS

The response rate was 78% (689 out of 881). The majority (88%; 607 out of 686) of physicians understood that antibiotic resistance was a local challenge. More than half (54%; 366 out of 682) believed that antibiotic prescribing was inappropriate in their hospital and 93% (638 out of 684) had difficulties in selecting appropriate antibiotics to treat common infections. The majority (86%; 574 out of 667) and one-third of physicians (36%; 236 out of 665) would prescribe antibiotics for uncomplicated common cold and diarrhea in children < 5 years of age, respectively. Half (58%; 385 out of 668) had experience treating methicillin-resistant Staphylococcus aureus infection, but the majority (73%; 188 out of 258) could not identify antibiotics to treat this infection. Only 17% (115 out of 667) had experience treating endemic melioidosis. All physicians agreed that knowledge about local antibiotic resistance, treatment guidelines, and educational programs were necessary.

CONCLUSIONS

Cambodian physicians are aware of antibiotic resistance challenges but they do not possess the required knowledge of local antibiotic resistance patterns that would assist their prescribing practices. Cambodian physicians need support to improve antibiotic prescribing.

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia

Typhoid fever, caused by the bacterium Salmonella Typhi, is an endemic cause of febrile disease in Cambodia. The aim of this study was to better understand the epidemiology of pediatric typhoid fever in Cambodia. We accessed routine blood culture data from Angkor Hospital for Children (AHC) in Siem Reap province between 2007 and 2014, and performed whole genome sequencing (WGS) on the isolated bacteria to characterize the S. Typhi population. The resulting phylogenetic information was combined with conventional epidemiological approaches to investigate the spatiotemporal distribution of S. Typhi and population-level risk factors for reported disease. During the study period, there were 262 cases of typhoid within a 100 km radius of AHC, with a median patient age of 8.2 years (IQR: 5.1-11.5 years). The majority of infections occurred during the rainy season, and commune incidences as high as 11.36/1,000 in children aged <15 years were observed over the study period. A population-based risk factor analysis found that access to water within households and increasing distance from Tonle Sap Lake were protective. Spatial mapping and WGS provided additional resolution for these findings, and confirmed that proximity to the lake was associated with discrete spatiotemporal disease clusters. We confirmed the dominance of MDR H58 S. Typhi in this population, and found substantial evidence of diversification (at least seven sublineages) within this single lineage. We conclude that there is a substantial burden of pediatric typhoid fever in rural communes in Cambodia. Our data provide a platform for additional population-based typhoid fever studies in this location, and suggest that this would be a suitable setting in which to introduce a school-based vaccination programme with Vi conjugate vaccines.

A novel broadly applicable PCR-RFLP method for rapid identification and subtyping of H58 Salmonella Typhi

Salmonella Typhi (S. Typhi), the human-adapted agent of typhoid fever, is genetically monomorphic. SNPs accumulation divided the S. Typhi population in 85 haplotypes (H) of which one, H58, has undergone a clonal expansion. The surveillance of H58 S. Typhi is particularly important, especially in areas where typhoid fever is endemic. We developed a simple PCR and PCR-RFLP method to detect and subtype H58 S. Typhi based on the presence of genomic deletion and specific SNPs. The method was validated against 39 S. Typhi isolates of known haplotype, showing 100% of specificity and high sensitivity, and then used to screen a collection of 99 S. Typhi from Asia, demonstrating a high incidence of H58 S. Typhi in Jordan and India. Our method is designed to be applied in all laboratories with basic molecular biology equipment and few financial resources and allows the surveillance of H58 S. Typhi in resource poor settings.

A retrospective study of factors which determine a negative blood culture in Cambodian children diagnosed with enteric fever

BACKGROUND

Blood cultures are used to confirm a diagnosis of enteric fever but reported sensitivities can be as low as 40%.

AIMS

To determine the factors associated with a negative blood culture in Cambodian children with suspected enteric fever.

METHODS

In a retrospective study of hospitalised Cambodian children given a discharge diagnosis of enteric fever, the following factors associated with a negative blood culture were analysed: age, blood culture volume, prior antibiotic therapy, duration of illness and disease severity.

RESULTS

In 227 hospitalised Cambodian children with a discharge diagnosis of enteric fever, it was confirmed in 70% by a positive blood culture. There was no association between a negative blood culture and younger age, lower blood volumes for culture, prior antibiotic therapy, a late presentation or milder disease.

CONCLUSIONS

Although blood culture sensitivity was higher than expected, alternative simple, rapid and sensitive tests are needed for diagnosing enteric fever.

A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure

The interplay between bacterial antimicrobial susceptibility, phylogenetics and patient outcome is poorly understood. During a typhoid clinical treatment trial in Nepal, we observed several treatment failures and isolated highly fluoroquinolone-resistant Salmonella Typhi (S. Typhi). Seventy-eight S. Typhi isolates were genome sequenced and clinical observations, treatment failures and fever clearance times (FCTs) were stratified by lineage. Most fluoroquinolone-resistant S. Typhi belonged to a specific H58 subclade. Treatment failure with S. Typhi-H58 was significantly less frequent with ceftriaxone (3/31; 9.7%) than gatifloxacin (15/34; 44.1%)(Hazard Ratio 0.19, p=0.002). Further, for gatifloxacin-treated patients, those infected with fluoroquinolone-resistant organisms had significantly higher median FCTs (8.2 days) than those infected with susceptible (2.96) or intermediately resistant organisms (4.01)(p<0.001). H58 is the dominant S. Typhi clade internationally, but there are no data regarding disease outcome with this organism. We report an emergent new subclade of S. Typhi-H58 that is associated with fluoroquinolone treatment failure.

Clinical trial registration: ISRCTN63006567.

DOI:http://dx.doi.org/10.7554/eLife.14003.001

People who ingest a type of bacteria called Salmonella Typhi can develop the symptoms of typhoid fever. This disease is common in low-income settings in Asia and Africa, and causes a high rate of death in people who are not treated with antimicrobial drugs.

During a study in Nepal, Thanh et al. tried to evaluate which of two antimicrobials was better for treating typhoid fever. One of the drugs – called gatifloxacin – did not work in some of the patients. To understand why this treatment failed, Thanh et al. decoded the entire DNA sequences of all the Salmonella Typhi bacteria isolated during the study. Comparing this genetic data to the clinical data of the patients identified a new variant of Salmonella Typhi. These bacteria have a specific combination of genetic mutations that render them resistant to the family of drugs that gatifloxacin belongs to – the fluoroquinolones.

Patients infected with the variant bacteria and treated with gatifloxacin were highly likely to completely fail treatment and have longer-lasting fevers. On further investigation Thanh et al. found these organisms were likely recently introduced into Nepal from India.

Fluoroquinolones are amongst the most effective and common antimicrobials used to treat typhoid fever and other bacterial infections. However, the presence of bacteria that are resistant to these compounds in South Asia means that they should no longer be the first choice of drug to treat typhoid fever in this location.

DOI:http://dx.doi.org/10.7554/eLife.14003.002

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.

Antibacterial efficacy of five medicinal plants against multidrug-resistant enteropathogenic bacteria infecting under-5 hospitalized children

OBJECTIVE

To evaluate in vitro antibacterial effectiveness of five medicinal plants used by an Indian aborigine, against 8 multidrug-resistant (MDR) enteropathogenic bacteria isolated from clinical samples of under-5 hospitalized children.

METHODS

Antibiotic sensitivity patterns of eight clinically isolated strains of enteropathogenic bacteria, Enterobacter aerogenes, Escherichia coli, Klebsiella pneumoniae, Salmonella paratyphi, S. typhi, Shigella dysenteriae, S. sonnei and Vibrio cholerae were assessed by disc-diffusion method. Antibacterial activities of 8 solvent-extracts of leaves and bark of five medicinal plants were monitored by the agar-well diffusion method. The microbroth dilution method was used to assess minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). Qualitative phytochemical analyses of active plant extracts were carried out.

RESULTS

Ethanol, ethyl acetate and methanol extracts of Holarrhena antidysenterica leaf tissue were most effective against 8 MDR pathogens in vitro. Similarly, acetone, ethanol and methanol extracts of Terminalia alata leaf tissue; chloroform, ethyl acetate and methanol extracts of Terminalia arjuna leaf tissue and ethyl acetate, ethanol and methanol extracts of Paederia foetida leaf tissue were most effective in inhibiting in vitro growth of the 8 MDR enteropathogens. Ethyl acetate and methanol extracts of H. antidysenterica bark tissue; acetone, ethanol and methanol extracts of T. alata bark tissue and acetone, ethanol and methanol extracts of T. arjuna bark tissue were most effective in controlling enteropathogen growth. The minimum inhibitory concentration and minimum bactericidal concentration values of the 3 most antimicrobial leaf and bark extracts from the five plants were in the range of 1.56 to 50 mg/mL.

CONCLUSION

These 5 plants exhibited in vitro control over a cohort of 8 enteropathogenic bacterial strains isolated from clinical samples.

A novel technique for detecting antibiotic-resistant typhoid from rapid diagnostic tests

Fluoroquinolone-resistant typhoid is increasing. An antigen-detecting rapid diagnotic test (RDT) can rapidly diagnose typhoid from blood cultures. A simple, inexpensive molecular technique performed with DNA from positive RDTs accurately identified gyrA mutations consistent with phenotypic susceptibility testing results. Field diagnosis combined with centralized molecular resistance testing could improve typhoid management and surveillance in low-resource settings.

Systematic Review of Antibiotic Resistance Rates Among Gram-Negative Bacteria in Children With Sepsis in Resource-Limited Countries

BACKGROUND

Gram-negative antimicrobial resistance (AMR) is of global concern, yet there are few reports from low- and low-middle-income countries, where antimicrobial choices are often limited.

METHODS

This study offers a systematic review of PubMed, Embase, and World Health Organization (WHO) regional databases of Gram-negative bacteremia in children in low- and low-middle-income countries reporting AMR since 2001.

RESULTS

Data included 30 studies comprising 71 326 children, of whom 7056 had positive blood cultures, and Gram-negative organisms were isolated in 4710 (66.8%). In neonates, Klebsiella pneumoniae median resistance to ampicillin was 94% and cephalosporins 84% in Asia; 100% and 50% in Africa. Large regional variations in resistance rates to commonly prescribed antibiotics for Salmonella spp. were identified. Multidrug resistance (resistance to ampicillin, chloramphenicol, and cotrimoxazole) was present in 30% (interquartile range [IQR], 0-59.6) in Asia and 75% (IQR, 30-85.4) in Africa.

CONCLUSIONS

There is a need for an international pediatric antimicrobial resistance surveillance system that collects local epidemiological data to improve the evidence base for the WHO guidance for childhood Gram-negative bacteremia.

Typhoid outbreak in Songkhla, Thailand 2009-2011: clinical outcomes, susceptibility patterns, and reliability of serology tests

Objective

To determine the clinical manifestations and outcomes, the reliability of Salmonella enterica serotype Typhi (S ser. Typhi) IgM and IgG rapid tests, and the susceptibility patterns and the response to treatment during the 2009–2011 typhoid outbreak in Songkhla province in Thailand.

Method

The medical records of children aged <15 years with S ser. Typhi bacteremia were analysed. The efficacy of the typhoid IgM and IgG rapid tests and susceptibility of the S ser. Typhi to the current main antibiotics used for typhoid (amoxicillin, ampicillin, cefotaxime, ceftriaxone, co-trimoxazole, and ciprofloxacin), were evaluated.

Results

S ser. Typhi bacteremia was found in 368 patients, and all isolated strains were susceptible to all 6 antimicrobials tested. Most of the patients were treated with ciprofloxacin for 7–14 days. The median time (IQR) of fever before treatment and duration of fever after treatment were 5 (4, 7) days and 4 (3, 5) days, respectively. Complications of ascites, lower respiratory symptoms, anemia (Hct <30%), and ileal perforation were found in 7, 7, 22, and 1 patients, respectively. None of the patients had recurrent infection or died. The sensitivities of the typhoid IgM and IgG tests were 58.3% and 25.6% respectively, and specificities were 74.1% and 50.5%, respectively.

Conclusion

Most of the patients were diagnosed at an early stage and treated with a good outcome. All S ser. Typhi strains were susceptible to standard first line antibiotic typhoid treatment. The typhoid IgM and IgG rapid tests had low sensitivity and moderate specificity.

Urinary antibiotic activity in paediatric patients attending an outpatient department in north-western Cambodia

Objective

Antibiotic resistance is a prominent public and global health concern. We investigated antibiotic use in children by determining the proportion of unselected children with antibacterial activity in their urine attending a paediatric outpatient department in Siem Reap, Cambodia.

Methods

Caregiver reports of medication history and presence of possible infection symptoms were collected in addition to urine samples. Urine antibiotic activity was estimated by exposing bacteria to urine specimens, including assessment against multiresistant bacteria previously isolated from patients in the hospital (a methicillin-resistant Staphylococcus aureus (MRSA), a multiresistant Salmonella typhi and an extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolate).

Results

Medication information and urine were collected from 775 children. Caregivers reported medication use in 69.0% of children in the preceding 48 h. 31.7% samples showed antibacterial activity; 16.3% showed activity against a local multiresistant organism. No specimens demonstrated activity against an ESBL-producing E. coli.

Conclusions

Antibiotics are widely used in the community setting in Cambodia. Parents are often ill-informed about drugs given to treat their children. Increasing the regulation and training of private pharmacies in Cambodia may be necessary. Regional surveillance of antibiotic use and resistance is also essential in devising preventive strategies against further development of antibiotic resistance, which would have both local and global consequences.

How multidrug resistance in typhoid fever affects treatment options

Salmonella enterica serotype Typhi (S. Typhi) is an enteric pathogen that causes typhoid fever. The infection can be severe, with significant morbidity and mortality, requiring antimicrobial therapy. Cases of S. Typhi infection in the United States and other developed countries are often associated with travel to endemic regions. The empirical use of first-line drugs for therapy, including ampicillin, chloramphenicol, and trimethoprim/sulfamethoxazole, has resulted in transmissible multidrug resistance. With the global increase in multidrug-resistant S. Typhi, use of ciprofloxacin, with excellent oral absorption, few side effects, and cost-effectiveness, has become popular for treatment. However, decreased ciprofloxacin susceptibility due to point mutations in the S. Typhi genes gyrA and/or parC has caused treatment failures, necessitating alternative therapeutic options. S. Typhi is typically genetically homogenous, with phylogenetic and epidemiological studies showing that identical clones and diverse S. Typhi types often coexist in the same geographic region. Studies investigating point mutations have demonstrated that selective pressure from empirical use of first-line drugs and fluoroquinolones has led to the global emergence of haplotype H-58. Antibiotic resistance is subject to high selective pressure in S. Typhi and thus demands careful use of antimicrobials.

Estimating the burden of paratyphoid a in Asia and Africa

Despite the increasing availability of typhoid vaccine in many regions, global estimates of mortality attributable to enteric fever appear stable. While both Salmonella enterica serovar Typhi (S. Typhi) and serovar Paratyphi (S. Paratyphi) cause enteric fever, limited data exist estimating the burden of S. Paratyphi, particularly in Asia and Africa.

We performed a systematic review of both English and Chinese-language databases to estimate the regional burden of paratyphoid within Africa and Asia. Distinct from previous reviews of the topic, we have presented two separate measures of burden; both incidence and proportion of enteric fever attributable to paratyphoid. Included articles reported laboratory-confirmed Salmonella serovar classification, provided clear methods on sampling strategy, defined the age range of participants, and specified the time period of the study.

A total of 64 full-text articles satisfied inclusion criteria and were included in the qualitative synthesis. Paratyphoid A was commonly identified as a cause of enteric fever throughout Asia. The highest incidence estimates in Asia came from China; four studies estimated incidence rates of over 150 cases/100,000 person-years. Paratyphoid A burden estimates from Africa were extremely limited and with the exception of Nigeria, few population or hospital-based studies from Africa reported significant Paratyphoid A burden.

While significant gaps exist in the existing population-level estimates of paratyphoid burden in Asia and Africa, available data suggest that paratyphoid A is a significant cause of enteric fever in Asia. The high variability in documented incidence and proportion estimates of paratyphoid suggest considerable geospatial variability in the burden of paratyphoid fever. Additional efforts to monitor enteric fever at the population level will be necessary in order to accurately quantify the public health threat posed by S. Paratyphi A, and to improve the prevention and treatment of enteric fever.

Enteric fever due to Salmonella enterica serovar Typhi (S. Typhi) and serovar Paratyphi (S. Paratyphi A, B, C) remains a global public health concern. While numerous studies have estimated the levels or burden of S. Typhi, there are only limited data estimating the burden of S. Paratyphi A, particularly in Asia and Africa. We reviewed both English and Chinese-language databases for estimates of the regional burden within Africa and Asia, including new paratyphoid A cases/year and proportion of enteric fever cases attributable to paratyphoid A. S. Paratyphi A appears to constitute a significant proportion of all cases of enteric fever in Asia, though population level estimates are limited, especially in Africa. There was high variability in reported paratyphoid A burden estimates, which suggests considerable geospatial variability in the burden of paratyphoid fever. Improved efforts to monitor enteric fever at the population level are warranted in order to correctly measure the public health threat posed by S. Paratyphi A and to determine the potential need for S. Paratyphi specific prevention and treatment interventions.

Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure

Fluoroquinolones (FQ) are the recommended antimicrobial treatment for typhoid, a severe systemic infection caused by the bacterium Salmonella enterica serovar Typhi. FQ-resistance mutations in S. Typhi have become common, hindering treatment and control efforts. Using in vitro competition experiments, we assayed the fitness of eleven isogenic S. Typhi strains with resistance mutations in the FQ target genes, gyrA and parC. In the absence of antimicrobial pressure, 6 out of 11 mutants carried a selective advantage over the antimicrobial-sensitive parent strain, indicating that FQ resistance in S. Typhi is not typically associated with fitness costs. Double-mutants exhibited higher than expected fitness as a result of synergistic epistasis, signifying that epistasis may be a critical factor in the evolution and molecular epidemiology of S. Typhi. Our findings have important implications for the management of drug-resistant S. Typhi, suggesting that FQ-resistant strains would be naturally maintained even if fluoroquinolone use were reduced.

DOI:http://dx.doi.org/10.7554/eLife.01229.001

The fluoroquinolones are a group of antimicrobials that are used to treat a variety of life-threatening bacterial infections, including typhoid fever. Before the introduction of antimicrobials, the mortality rate from typhoid fever was 10–20%. Prompt treatment with fluoroquinolones has reduced this to less than 1%, and has also decreased the severity of symptoms suffered by people with the disease.

Now, however, the usefulness of many antimicrobials, including the fluoroquinolones, is threatened by the evolution of antimicrobial resistance within the bacterial populations being treated. Drug resistance in bacteria typically arises through specific mutations, or following the acquisition of antimicrobial resistance genes from other bacteria. It is thought that the frequent use of antimicrobials in human and animal health puts selective pressure on bacterial populations, allowing bacterial strains with mutations or genes that confer antimicrobial resistance to survive, while bacterial strains that are sensitive to the antimicrobials die out.

At first it was thought that specific mutations conferring antimicrobial resistance came at a fitness cost, which would mean that such mutations would be rare in the absence of antimicrobials. Now, based on research into typhoid fever, Baker et al. describe a system in which the majority of evolutionary routes to drug resistance are marked by significant fitness benefits, even in the absence of antimicrobial exposure.

Typhoid is caused by a bacterial pathogen known as Salmonella Typhi, and mutations in two genes—gyrA and parC—result in resistance to fluoroquinolones. Baker et al. show that mutations in these genes confer a measurable fitness advantage over strains without these mutations, even in the absence of exposure to fluoroquinolones. Moreover, strains with two mutations in one of these genes exhibited a higher than predicted fitness, suggesting that there is a synergistic interaction between the two mutations. This work challenges the dogma that antimicrobial resistant organisms have a fitness disadvantage in the absence of antimicrobials, and suggests that increasing resistance to the fluoroquinolones is not solely driven by excessive use of this important group of drugs.

DOI:http://dx.doi.org/10.7554/eLife.01229.002

Evaluation of the diagnostic accuracy of a typhoid IgM flow assay for the diagnosis of typhoid fever in Cambodian children using a Bayesian latent class model assuming an imperfect gold standard

Rapid diagnostic tests are needed for typhoid fever (TF) diagnosis in febrile children in endemic areas. Five hundred children admitted to the hospital in Cambodia between 2009 and 2010 with documented fever (≥ 38°C) were investigated using blood cultures (BCs), Salmonella Typhi/Paratyphi A real-time polymerase chain reactions (PCRs), and a Typhoid immunoglobulin M flow assay (IgMFA). Test performance was determined by conventional methods and Bayesian latent class modeling. There were 32 cases of TF (10 BC- and PCR-positive cases, 14 BC-positive and PCR-negative cases, and 8 BC-negative and PCR-positive cases). IgMFA sensitivity was 59.4% (95% confidence interval = 41–76), and specificity was 97.8% (95% confidence interval = 96–99). The model estimate sensitivity for BC was 81.0% (95% credible interval = 54–99). The model estimate sensitivity for PCR was 37.8% (95% credible interval = 26–55), with a specificity of 98.2% (95% credible interval = 97–99). The model estimate sensitivity for IgMFA (≥ 2+) was 77.9% (95% credible interval = 58–90), with a specificity of 97.5% (95% credible interval = 95–100). The model estimates of IgMFA sensitivity and specificity were comparable with BCs and better than estimates using conventional analysis.

A prospective study of the causes of febrile illness requiring hospitalization in children in Cambodia

Background

Febrile illnesses are pre-eminent contributors to morbidity and mortality among children in South-East Asia but the causes are poorly understood. We determined the causes of fever in children hospitalised in Siem Reap province, Cambodia.

Methods and Findings

A one-year prospective study of febrile children admitted to Angkor Hospital for Children, Siem Reap. Demographic, clinical, laboratory and outcome data were comprehensively analysed. Between October 12^th 2009 and October 12^th 2010 there were 1225 episodes of febrile illness in 1180 children. Median (IQR) age was 2.0 (0.8–6.4) years, with 850 (69%) episodes in children <5 years. Common microbiological diagnoses were dengue virus (16.2%), scrub typhus (7.8%), and Japanese encephalitis virus (5.8%). 76 (6.3%) episodes had culture-proven bloodstream infection, including Salmonella enterica serovar Typhi (22 isolates, 1.8%), Streptococcus pneumoniae (13, 1.1%), Escherichia coli (8, 0.7%), Haemophilus influenzae (7, 0.6%), Staphylococcus aureus (6, 0.5%) and Burkholderia pseudomallei (6, 0.5%). There were 69 deaths (5.6%), including those due to clinically diagnosed pneumonia (19), dengue virus (5), and melioidosis (4). 10 of 69 (14.5%) deaths were associated with culture-proven bloodstream infection in logistic regression analyses (odds ratio for mortality 3.4, 95% CI 1.6–6.9). Antimicrobial resistance was prevalent, particularly in S. enterica Typhi, (where 90% of isolates were resistant to ciprofloxacin, and 86% were multi-drug resistant). Comorbid undernutrition was present in 44% of episodes and a major risk factor for acute mortality (OR 2.1, 95% CI 1.1–4.2), as were HIV infection and cardiac disease.

Conclusion

We identified a microbiological cause of fever in almost 50% of episodes in this large study of community-acquired febrile illness in hospitalized children in Cambodia. The range of pathogens, antimicrobial susceptibility, and co-morbidities associated with mortality described will be of use in the development of rational guidelines for infectious disease treatment and control in Cambodia and South-East Asia.