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.

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

Enteric fever, an infection caused by Salmonella enterica serovar Typhi and serovar Paratyphi A, is common and endemic in many areas of the Asian and African continents. In endemic areas, diagnostic tests are needed to diagnose acute cases for clinical management, to detect convalescent and chronic fecal carriage and for contact tracing. A suitable test may also allow an assessment of disease burden in a community to determine the need for vaccination programs. Each specific role may warrant a dedicated test, utilizing different samples, targets and methods to serve their respective purpose. Current diagnostic methods are poor. Blood culture is insufficiently sensitive and technically demanding, and bone marrow culture, although more sensitive, is infrequently performed. Antibody- and antigen-detection tests lend themselves to point-of-care format but remain insufficiently sensitive and specific for this role. There are concerns about the sensitivity of nucleic acid amplification tests and they have not b...

https://www.tandfonline.com/doi/pdf/10.1586/eri.11.47

The utility of diagnostic tests for enteric fever in endemic locations

Background
Differentiating both typhoid (Salmonella Typhi) and paratyphoid (Salmonella Paratyphi A) infection from other causes of fever in endemic areas is a diagnostic challenge. Although commercial point-of-care rapid diagnostic tests (RDTs) for enteric fever are available as alternatives to the current reference standard test of blood or bone marrow culture, or to the widely used Widal Test, their diagnostic accuracy is unclear. If accurate, they could potentially replace blood culture as the World Health Organization (WHO)-recommended main diagnostic test for enteric fever.

Objectives
To assess the diagnostic accuracy of commercially available rapid diagnostic tests (RDTs) and prototypes for detecting Salmonella Typhi or Paratyphi A infection in symptomatic persons living in endemic areas.

Search methods
We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, IndMED, African Index Medicus, LILACS, ClinicalTrials.gov, and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) up to 4 March 2016. We manually searched WHO reports, and papers from international conferences on Salmonella infections. We also contacted test manufacturers to identify studies.

Selection criteria
We included diagnostic accuracy studies of enteric fever RDTs in patients with fever or with symptoms suggestive of enteric fever living in endemic areas. We classified the reference standard used as either Grade 1 (result from a blood culture and a bone marrow culture) or Grade 2 (result from blood culture and blood polymerase chain reaction, or from blood culture alone).

Data collection and analysis
Two review authors independently extracted the test result data. We used a modified QUADAS-2 extraction form to assess methodological quality. We performed a meta-analysis when there were sufficient studies for the test and heterogeneity was reasonable.

Main results
Thirty-seven studies met the inclusion criteria and included a total of 5080 participants (range 50 to 1732). Enteric fever prevalence rates in the study populations ranged from 1% to 75% (median prevalence 24%, interquartile range (IQR) 11% to 46%). The included studies evaluated 16 different RDTs, and 16 studies compared two or more different RDTs. Only three studies used the Grade 1 reference standard, and only 11 studies recruited unselected febrile patients. Most included studies were from Asia, with five studies from sub-Saharan Africa. All of the RDTs were designed to detect S.Typhi infection only.

Most studies evaluated three RDTs and their variants: TUBEX in 14 studies; Typhidot (Typhidot, Typhidot-M, and TyphiRapid-Tr02) in 22 studies; and the Test-It Typhoid immunochromatographic lateral flow assay, and its earlier prototypes (dipstick, latex agglutination) developed by the Royal Tropical Institute, Amsterdam (KIT) in nine studies. Meta-analyses showed an average sensitivity of 78% (95% confidence interval (CI) 71% to 85%) and specificity of 87% (95% CI 82% to 91%) for TUBEX; and an average sensitivity of 69% (95% CI 59% to 78%) and specificity of 90% (95% CI 78% to 93%) for all Test-It Typhoid and prototype tests (KIT). Across all forms of the Typhidot test, the average sensitivity was 84% (95% CI 73% to 91%) and specificity was 79% (95% CI 70% to 87%). When we based the analysis on the 13 studies of the Typhidot test that either reported indeterminate test results or where the test format means there are no indeterminate results, the average sensitivity was 78% (95% CI 65% to 87%) and specificity was 77% (95% CI 66% to 86%). We did not identify any difference in either sensitivity or specificity between TUBEX, Typhidot, and Test-it Typhoid tests when based on comparison to the 13 Typhidot studies where indeterminate results are either reported or not applicable. If TUBEX and Test-it Typhoid are compared to all Typhidot studies, the sensitivity of Typhidot was higher than Test-it Typhoid (15% (95% CI 2% to 28%), but other comparisons did not show a difference at the 95% level of CIs.

In a hypothetical cohort of 1000 patients presenting with fever where 30% (300 patients) have enteric fever, on average Typhidot tests reporting indeterminate results or where tests do not produce indeterminate results will miss the diagnosis in 66 patients with enteric fever, TUBEX will miss 66, and Test-It Typhoid and prototype (KIT) tests will miss 93. In the 700 people without enteric fever, the number of people incorrectly diagnosed with enteric fever would be 161 with Typhidot tests, 91 with TUBEX, and 70 with Test-It Typhoid and prototype (KIT) tests. The CIs around these estimates were wide, with no difference in false positive results shown between tests.

The quality of the data for each study was evaluated using a standardized checklist called QUADAS-2. Overall, the certainty of the evidence in the studies that evaluated enteric fever RDTs was low.

Authors' conclusions
In 37 studies that evaluated the diagnostic accuracy of RDTs for enteric fever, few studies were at a low risk of bias. The three main RDT tests and variants had moderate diagnostic accuracy. There was no evidence of a difference between the average sensitivity and specificity of the three main RDT tests. More robust evaluations of alternative RDTs for enteric fever are needed.

/pdf/rapid-diagnostic-tests-for-typhoid-and-paratyphoid-enteric-1bwcmwbor7.pdf

Rapid diagnostic tests for typhoid and paratyphoid (enteric) fever.

Bacterial enteric infections resulting in diarrhea, dysentery, or enteric fever constitute a huge public health problem, with more than a billion episodes of disease annually in developing and developed countries. In this study, the deadly agent of hemorrhagic diarrhea and hemolytic uremic syndrome, Escherichia coli O157:H7 was investigated with extensive computational approaches aimed at identifying novel and broad-spectrum antibiotic targets. A systematic in silico workflow consisting of comparative genomics, metabolic pathways analysis, and additional drug prioritizing parameters was used to identify novel drug targets that were essential for the pathogen's survival but absent in its human host. Comparative genomic analysis of Kyoto Encyclopedia of Genes and Genomes annotated metabolic pathways identified 350 putative target proteins in E. coli O157:H7 which showed no similarity to human proteins. Further bio-informatic approaches including prediction of subcellular localization, calculation of molecular weight, and web-based investigation of 3D structural characteristics greatly aided in filtering the potential drug targets from 350 to 120. Ultimately, 44 non-homologous essential proteins of E. coli O157:H7 were prioritized and proved to have the eligibility to become novel broad-spectrum antibiotic targets and DNA polymerase III alpha (dnaE) was the top-ranked among these targets. Moreover, druggability of each of the identified drug targets was evaluated by the DrugBank database. In addition, 3D structure of the dnaE was modeled and explored further for in silico docking with ligands having potential druggability. Finally, we confirmed that the compounds N-coeleneterazine and N-(1,4-dihydro-5H-tetrazol-5-ylidene)-9-oxo-9H-xanthene-2-sulfon-amide were the most suitable ligands of dnaE and hence proposed as the potential inhibitors of this target protein. The results of this study could facilitate the discovery and release of new and effective drugs against E. coli O157:H7 and other deadly human bacterial pathogens.

/pdf/identification-of-potential-drug-targets-by-subtractive-4auyyazk3u.pdf

Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach

Global growth in antibiotic resistance is a major social problem. A high level of resistance to fluoroquinolones requires the concurrent presence of at least 3 mutations in the target proteins-2 in DNA gyrase (GyrA) and 1 in topoisomerase IV (ParC), which occur in a stepwise manner. In the Escherichia coli chromosome, the gyrA and parC loci are positioned about 1 Mb away from each other. Here we show that the 3 fluoroquinolone resistance mutations are tightly associated genetically in naturally occurring strains. In the latest pandemic uropathogenic and multidrug-resistant E. coli clonal group ST1193, the mutant variants of gyrA and parC were acquired not by a typical gradual, stepwise evolution but all at once. This happened as part of 11 simultaneous homologous recombination events involving 2 phylogenetically distant strains of E. coli, from an uropathogenic clonal complex ST14 and fluoroquinolone-resistant ST10. The gene exchanges swapped regions between 0.5 and 139 Kb in length (183 Kb total) spread along 976 Kb of chromosomal DNA around and between gyrA and parC loci. As a result, all 3 fluoroquinolone resistance mutations in GyrA and ParC have simultaneously appeared in ST1193. Based on molecular clock estimates, this potentially happened as recently as <12 y ago. Thus, naturally occurring homologous recombination events between 2 strains can involve numerous chromosomal gene locations simultaneously, resulting in the transfer of distant but tightly associated genetic mutations and emergence of a both highly pathogenic and antibiotic-resistant strain with a rapid global spread capability.

Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci.

Summary
Co-agglutination (coagg) and latex agglutination (LA) tests were used for the detection of Salmonella serotype Typhi Vi and Barber protein (BP) antigens in sera from five groups of individuals (A–E). Group A consisted of 30 blood culture-positive cases of typhoid fever and group B consisted of 30 suspected cases of typhoid fever who had sterile blood cultures but positive Widal tests. Thirty cases of pyrexia of unknown origin (PUO) were placed in group C, while group D consisted of 15 cases of septicaemia caused by organisms other than Salmonella serotype Typhi. Group E comprised 50 normal healthy individuals with no history of typhoid fever or TAB vaccination in the previous 5 years. The Vi-LA test performed best with 96·7% of group A sera and 90% of group B sera giving positive results. No false positive results and only 2·58% false negative results were obtained with this test. Considering patients with positive blood culture results or positive Widal tests as true positives, the sensitivities of the Vi-LA, BP-LA, Vi-coagg and BP-coagg tests were 93·3, 91·7, 83-3 and 86·7%, respectively. The specificities of these tests were 100, 98·5, 98·5 and 98·5%, respectively. It is suggested that the Vi-LA test can be used for the rapid and early diagnosis of typhoid fever.

/pdf/rapid-diagnosis-of-typhoid-fever-by-detection-of-barber-34qt8yai7k.pdf

Rapid diagnosis of typhoid fever by detection of Barber protein and Vi antigen of Salmonella serotype Typhi

Yokenella regensburgei is an opportunistic human pathogen of the Enterobacteriaceae family rarely reported to cause human infections. Here, we present a case report of Y. regensburgei bacteraemia from India clinically resembling enteric fever in an apparently immunocompetent paediatric patient.

Yokenella regensburgei infection in India mimicking enteric fever.

Case Report Yokenella regensburgei infection in India mimicking enteric fever

Background The emergence of resistance amongst commensal flora is a serious threat to the community However, there is paucity of data regarding antibiotic resistance in commensals in the absence of antibiotic pressure Methods Altogether, 100 vaginally delivered antibiotic naive exclusively breastfed neonates were selected Stool samples collected on day (D)1, D21 and D60 of birth were cultured Enterobacteriaceae isolates were screened for nalidixic acid (NA) and ciprofloxacin susceptibility as per CLSI guidelines In 28 randomly selected neonates, isolates (n=92) resistant to NA and ciprofloxacin were characterized for the presence of plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB and qnrS, qepAand aac(6′)-Ib-cr) and mutations in the quinolone resistance determining region (QRDR) of gyrA and parC genes by specific primers and confirmed by sequencing Results A total of 343 Enterobacteriaceae were isolated from 100 neonates On D1, 58 % of neonates were colonized with at least one Enterobacteriaceae predominantly E coli Overall resistance to NA was 60 % but ciprofloxacin resistance increased significantly from 15 % (14/96) on D1 to 38 % (50/132) on D60 (P-value <0001) The predominant mechanism of fluoroquinolone resistance was mutation in gyrA (n=49) with or without PMQR PMQR carrying isolates increased more than fivefold from D1 to D60 Conclusion A high level of fluoroquinolone resistance in gut flora of antibiotic naive and exclusively breastfed neonates suggests a rampant rise of resistance in the community The source of resistance genes on D1 is probably maternal flora acquired at birth High load of PMQR genes in commensal flora are a potential source of spread to pathogenic organisms

Manorama Deb

Papers

Rapid diagnosis of typhoid fever by detection of Barber protein and Vi antigen of Salmonella serotype Typhi

Yokenella regensburgei infection in India mimicking enteric fever.

Case Report Yokenella regensburgei infection in India mimicking enteric fever

High prevalence of fluoroquinolone resistance amongst commensal flora of antibiotic naïve neonates: a study from India.