Reduced susceptibility to ciprofloxacin and gyra gene mutation in North Indian strains of Salmonella enterica serotype Typhi and serotype Paratyphi A

Ceftriaxone-resistant Salmonella Typhi isolated from paediatric patients in north India: Insights into genetic profiles and antibiotic resistance mechanisms

PURPOSE

To investigate the antibiotic resistance and genetic profile of ceftriaxone-resistant Salmonella Typhi isolated from the blood culture of two paediatric cases of typhoid fever and one from the stool culture of their household contact, in North India.

METHODS

In this study, whole-genome sequencing was carried out with paired-end 2 ​× ​150 bp reads on Illumina MiSeq (Illumina, USA) employing v2 and v3 chemistry. To check data quality, adapters and low-quality sequences were removed through Trimmomatic-v0.36. High quality reads were then assembled de novo using A5-miseq pipeline. For further refinement, reference-guided contig ordering and orienting were performed on the scaffold assemblies using ABACAS (http://abacas.sourceforge.net/). The assembled genome was annotated using Prokka v1.12 to identify and annotate the gene content. Plasmid replicons in bacterial isolates were identified by PlasmidFinder, whereas mobile genetic elements were predicted using Mobile Element Finder. Referenced-based SNP tree with maximum likelihood method was built with CSI phylogeny v1.4.

RESULTS

All three isolates exhibited resistance to ceftriaxone, cefixime, ciprofloxacin, ampicillin, and co-trimoxazole, while demonstrating sensitivity to azithromycin and chloramphenicol. The whole-genome sequencing of these strains revealed the presence of blaCTX-M-15 gene for cephalosporin resistance in addition to gyrA, qnr and IncY plasmid replicon. A 5 ​kb IS91 Sbo1 gene cassette (IncY plasmid) was identified which carried extended spectrum β-lactamase blaCTX-M-15, blaTEM-1D (resistance to ampicillin and cephalosporin), sul2, dfrA14 (resistant to trimethoprim-sulfamethoxazole) and qnrS (resistant to ciprofloxacin). These isolates belong to H58 lineage and grouped as sequence type 1 (ST1) on multilocus sequence typing (MLST) analysis.

CONCLUSION

In the present study we report the isolation of blaCTX-M-15 positive S. Typhi from two paediatric patients presenting with fever and one from stool culture of their contact from North India and highlight the need for further investigations to understand the different factors contributing to ceftriaxone resistance in Salmonella Typhi.

Genomic Characterization of Salmonella enterica Resistant to Cephalosporin, Quinolones, And Macrolides

Salmonella enterica subsp. enterica (Salmonella), one of the most common causes of bacterial foodborne infections, causes salmonellosis, which is usually self-limiting. However, immunocompromised individuals and children often require antimicrobial therapy. The first line of treatment includes fluoroquinolones, to which Salmonella has emerging resistance worldwide. In fact, the WHO classified fluoroquinolone-resistant Salmonella as a high-priority pathogen. Salmonella carrying genes such as blaCTX and blaCMY can show resistance to cephalosporins which are also regularly used for treatment. This study focused on determining the antimicrobial resistance of 373 Salmonella isolates, collected from various foods, humans, and animals, as well as the environmental sludge between 2005 and 2020 in Türkiye. Phenotypic analysis of the resistance was determined by disk diffusion method. Isolates resistant to any of the following: ciprofloxacin, pefloxacin, azithromycin, and ceftriaxone were tested for the presence of quinolone, beta-lactamase, and/or macrolide resistance genes by PCR and gel electrophoresis. Five multi-drug-resistant isolates were then further whole genome sequenced and analyzed. More than 32% (n = 120) of the isolates showed resistance to fluoroquinolones by disc diffusion. A significant number of quinolone-resistant isolates are presented with mutated parC and gyrA. Furthermore, 42% (n = 106) of the isolates were resistant to azithromycin and 10% of them harbored mphA gene. On the bright side, only eight isolates showed resistance to ceftriaxone. Overall, we observed an increase in the number of isolates showing resistance to fluoroquinolones and azithromycin over the years and low resistance to ceftriaxone.

Effect of Nanoencapsulation on the Antimicrobial and Antibiofilm Activities of Algerian Origanum glandulosum Desf. against Multidrug-Resistant Clinical Isolates

The emergence of multidrug-resistant (MDR) bacteria is a danger to public health and exposes patients to high risk, increasing morbidity and mortality worldwide. For this purpose, three months of evaluation of MDR’s prevalence and antimicrobial susceptibility patterns in the military regional university hospital of Constantine from different services and samples was carried out. Among a total of 196 isolates, 35.2% were MDR. The use of essential oils such as Origanum glandulosum Desf. as an alternative to antibiotics is attractive due to their rich content of bioactive compounds conferring many biological activities. Also, to overcome the drawbacks of using oils as the hydrophobicity and negative interaction with the environmental conditions, in addition to increasing their activity, encapsulation for the oil was performed using high-speed homogenization (HSH) into nanocapsules and high-pressure homogenization (HPH) into nanoemulsion. Nine volatile constituents were determined using gas chromatography-mass spectrometry analysis (GC-MS) in hydrodistilled oil with thymol, carvacrol, p-cymene, and γ-terpinene as dominants. A dramatic decrease in the major volatile components was observed due to the use of HSH and HPH but generated the same oil profile. The mean particle size of the nanoemulsion was 54.24 nm, while that of nanocapsules was 120.60 nm. The antibacterial activity of the oil and its nanoparticles was estimated on MDR isolates using the disk diffusion, aromatogram, and broth microdilution methods. Consistent with the differences in volatile constituents, the oil exhibited a higher antibacterial activity compared to its nanoforms with the diameters of the inhibition zone against E. coli (20 mm), S. aureus (35 mm), and A. baumannii (40 mm). Both formulations have shown relatively significant activity against the biofilm state at sub-inhibitory concentrations, where nanoemulsion was more potent than nanocapsules. The results obtained suggested that nanoformulations of essential oils are strongly recommended for therapeutic application as alternatives to antibiotics.

Ceftriaxone treatment failure in two cases of Enteric Fever caused by CTX-M15 positive Salmonella Typhi and its gastrointestinal carriage

We report two cases of culture positive typhoid fever caused by ceftriaxone resistant Salmonella Typhi. Bacterial isolates from both the cases were positive for ESBL by phenotypic methods. Both patients didn't respond to ceftriaxone and were finally treated with meropenem. Screening of family members of one patient isolated a similar strain from a healthy carrier with the same antibiogram pattern. All isolates were subjected to PCR, which confirmed the presence of blaCTX-M15 ESBL gene. These two cases confirm emergence of ESBL-producing Salmonella Typhi causing Enteric Fever in India and also their presence in the gut flora of healthy carriers.

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.

Antimicrobial Resistance in Salmonella Typhi Isolated From a Referral Hospital of Kathmandu, Nepal

Purpose:

The morbidity and mortality due to typhoid fever can be significantly reduced with the use of effective antibiotics. At present, fluoroquinolones, third generation cephalosporins, and azithromycin are widely used to treat typhoid fever. However, changing antibiotic susceptibility among Salmonella Typhi and Salmonella Paratyphi poses a particular challenge to the therapeutic management of enteric fever. The objective of this study was to assess the antibiotic susceptibility pattern of Salmonella Typhi isolates.

Patients and Methods:

A total of 706 blood specimens were collected from febrile patients attending the outpatient department of Kathmandu Model Hospital during June to September, 2018. The antibiotic susceptibility testing for 11 different antibiotics (nalidixic acid, ciprofloxacin, ofloxacin, levofloxacin, cefixime, ceftriaxone, cefotaxime, azithromycin, cotrimoxazole, chloramphenicol, and amoxicillin) was performed by disk diffusion method. Furthermore, minimum inhibitory concentration (MIC) values of ciprofloxacin, ofloxacin, and azithromycin were determined by agar dilution method. Mutation at gyrA ser83 associated with reduced susceptibility to fluoroquinolones was determined by PCR-RFLP.

Results:

Out of 706 blood samples, 6.94% (n = 49) were culture positive for Salmonella enterica (S. Typhi, n = 46). It was revealed that 97.8% S. Typhi isolates were susceptible to conventional first-line antibiotics (ampicillin, chloramphenicol, and cotrimoxazole), 97.3% to cephalosporins and 95.7% to azithromycin. S. Typhi were either resistant or intermediately susceptible to fluoroquinolones: 97.8% to ciprofloxacin, 91.3% to ofloxacin, and 89.1% to levofloxacin. The MIC of ciprofloxacin, ofloxacin, and azithromycin for S. Typhi ranged from 0.008 to 32, 0.03 to 16, and 2 to 8 μg/mL, respectively. Out of 46 S. Typhi isolates, 44 (95.65%) had gyrA ser83 mutation.

Conclusion:

Fluoroquinolones have poor activity against Salmonella Typhi. The trends of increasing azithromycin MIC value among S. Typhi might limit its use for the treatment of typhoid fever. Effectiveness of conventional first-line antibiotics in vitro suggests considering their clinical use after large-scale studies.

Mutational Diversity in the Quinolone Resistance-Determining Regions of Type-II Topoisomerases of Salmonella Serovars

Quinolone resistance in bacterial pathogens has primarily been associated with mutations in the quinolone resistance-determining regions (QRDRs) of bacterial type-II topoisomerases, which are DNA gyrase and topoisomerase IV. Depending on the position and type of the mutation (s) in the QRDRs, bacteria either become partially or completely resistant to quinolone. QRDR mutations have been identified and characterized in Salmonella enterica isolates from around the globe, particularly during the last decade, and efforts have been made to understand the propensity of different serovars to carry such mutations. Because there is currently no thorough analysis of the available literature on QRDR mutations in different Salmonella serovars, this review aims to provide a comprehensive picture of the mutational diversity in QRDRs of Salmonella serovars, summarizing the literature related to both typhoidal and non-typhoidal Salmonella serovars with a special emphasis on recent findings. This review will also discuss plasmid-mediated quinolone-resistance determinants with respect to their additive or synergistic contributions with QRDR mutations in imparting elevated quinolone resistance. Finally, the review will assess the contribution of membrane transporter-mediated quinolone efflux to quinolone resistance in strains carrying QRDR mutations. This information should be helpful to guide the routine surveillance of foodborne Salmonella serovars, especially with respect to their spread across countries, as well as to improve laboratory diagnosis of quinolone-resistant Salmonella strains.

Screening of natural compounds for identification of novel inhibitors against β-lactamase CTX-M-152 reported among Kluyvera georgiana isolates: An in vitro and in silico study

Multidrug resistance due to the expression of extended spectrum β-lactamases (ESBLs) by bacterial pathogens is an alarming health concern with huge socio-economic burden. Here, 102 bacterial isolates from Wastewater treatment plants (WTPs) were screened for resistance to different antibiotics. Kirby-Bauer method and phenotypic disc confirmatory test confirmed the prevalence of 20 ESBLs. Polymerase chain reaction-based detection confirmed 11 bla_CTX-M positive bacterial isolates. Genotyping of bacterial isolates by 16S rRNA gene sequencing showed the dissemination of bla_CTX-M in Escherichia fergusonii, Escherichia coli, Shigella sp., Kluyvera georgiana and Enterobacter sp. Amongst Kluyvera georgiana isolates, two were harboring bla_CTX-M-152. The 3D model of CTX-M-152 protein was generated using SwissProt and characterized by Ramachandran plot and SAVES. A library of natural compounds was screened to identify novel CTX-M-152 inhibitor(s). High-throughput virtual screening (HTVS), standard precision (SP) and extra precision (XP) docking led to the identification of five natural compounds (Naringin dihydrochalcone, Salvianolic acid B, Inositol, Guanosine and Ellagic acid) capable of binding to active site of CTX-M-152. Futher, characterization by MM-GBSA (Molecular Mechanism General Born Surface Area), and ADMET (Adsorption, Distribution, Metabolism, Excretion and Toxicity) showed that Ellagic acid was the most potent inhibitor of CTX-M-152. Molecular dynamics simulation also confirmed that Ellagic acid form a stable complex with CTX-M-152. The ability of Ellagic acid to inhibit growth of bacteria harboring CTX-M-152 was confirmed by MIC (Minimum Inhibitory Concentration; broth dilution method) and Zone of Inhibition (ZOI) studies with respect to Cefotaxime. The identification of a novel inhibitor of CTX-M-152 from a natural source holds promise for employment in the control of bacterial infections.

Structure based drug discovery and in vitro activity testing for DNA gyrase inhibitors of Salmonella enterica serovar Typhi

The emerged resistance in Typhoidal Salmonella has limited the treatment options for typhoid fever. In this scenario, there is a need to find alternate treatment modalities against this pathogen. Amongst the therapeutic agents currently being used to treat enteric fever, quinolones have enjoyed considerable success since past three decades. These drugs act upon DNA gyrase and the acquired resistance is due to mutations at Ser83 and Asp87 of gyrase A subunit. In the present study DNA gyrase enzyme was targeted to seek out potential new inhibitors which are not affected by these mutations. Molecular modelling and docking studies were performed in Schrödinger's molecular modelling software. Homology model of DNA gyrase-DNA complex was built using templates 1AB4 and 3LTN. Molecular dynamic simulations were performed in SPC solvent for 100 ns. Total 17,900,742 drug like molecules were downloaded from ZINC library of chemical compounds. The Glide XP score of the compounds ranged from -5.285 to -13.692. All the ligands bound at the four base pair staggered nick in the DNA binding groove of DNA gyrase enzyme with their aromatic rings intercalating between the bases of two successive nucleotides stabilized by π - π stacking interactions. The binding pocket of DNA gyrase B comprising conserved residues Lys 447, Gly 448, Lys 449, Ile 450, Leu 451, Gln 465 and Val 467 interacts with the ligand molecules through van der Waals interactions. The MIC (minimum inhibitory concentration), MBC (minimum bactericidal concentration) and IC₅₀ of the tested compounds ranged from 500 to 125 mg/L, 750 to 500 mg/L and 100 to 12.5 mg/L, respectively. The selected hits bind to quinolone binding pocket, but their mode of binding and conformation is different to fluoroquinolones, and hence, their binding is not affected by mutations at Ser83 or Asp87 positions. These lead compounds can be further explored as a scaffold to design inhibitors against DNA gyrase to bypass quinolone resistance.

Genomic profiling of antimicrobial resistance genes in clinical isolates of Salmonella Typhi from patients infected with Typhoid fever in India

The development of multidrug resistance in Salmonella enterica serovar Typhi currently forms a major roadblock for the treatment of enteric fever. This poses a major health problem in endemic regions and extends to travellers returning from developing countries. The appearance of fluoroquinolone non-susceptible strains has resulted in use of ceftriaxone as drug of choice with azithromycin being recommended for uncomplicated cases of typhoid fever. A recent sporadic instance of decreased susceptibility to the latest drug regime has necessitated a detailed analysis of antimicrobial resistance genes and possible relationships with their phenotypes to facilitate selection of future treatment regimes. Whole genome sequencing (WGS) was conducted for 133 clinical isolates from typhoid patients. Sequence output files were processed for pan-genome analysis and prediction of antimicrobial resistance genes. The WGS analyses disclosed the existence of fluoroquinolone resistance conferring mutations in gyrA, gyrB, parC and parE genes of all strains. Acquired resistance determining mechanisms observed included catA1 genes for chloramphenicol resistance, dfrA7, dfrA15, sul1 and sul2 for trimethoprim-sulfamethoxazole and bla_TEM-116/bla_TEM-1B genes for amoxicillin. No resistance determinants were found for ceftriaxone and cefixime. The genotypes were further correlated with their respective phenotypes for chloramphenicol, ampicillin, co-trimoxazole, ciprofloxacin and ceftriaxone. A high correlation was observed between genotypes and phenotypes in isolates of S. Typhi. The pan-genome analysis revealed that core genes were enriched in metabolic functions and accessory genes were majorly implicated in pathogenesis and antimicrobial resistance. The pan-genome of S. Typhi appears to be closed (B_pan  =  0.09) as analysed by Heap’s law. Simpson’s diversity index of 0.51 showed a lower level of genetic diversity among isolates of S. Typhi. Overall, this study augments the present knowledge that WGS can help predict resistance genotypes and eventual correlation with phenotypes, enabling the chance to spot AMR determinants for fast diagnosis and prioritize antibiotic use directly from sequence.

A systematic review of antimicrobial resistance of typhoidal Salmonella in India

Background & objectives:

The temporal trends in the development of antimicrobial resistance (AMR) among Salmonella Typhi and Salmonella Paratyphi in India have not been systematically reported. We aimed to systematically review the temporal AMR trends (phenotypic and molecular mechanisms) in bacterial isolates from patients with enteric fever over two decades in India.

Methods:

To identify trends in AMR in India, resistance patterns among 4611 individual S. Typhi isolates and 800 S. Paratyphi A isolates, reported from 1992 to 2017 in 40 publications, were analysed. Molecular resistance determinants were extracted from 22 publications and also reviewed in accordance with the PRISMA guidelines. Articles were sourced using a predefined search strategy from different databases.

Results:

The analyses suggested that multidrug-resistant (MDR) enteric fever was declining in India and being replaced by fluoroquinolone (FQ) resistance. Mutations in gyrA and parC were key mechanisms responsible for FQ resistance, whereas MDR was largely driven by resistance determinants encoded on mobile genetic elements (plasmids, transposons).

Interpretation & conclusions:

The results reflect the effect of antimicrobial pressure which has been driving AMR in typhoidal Salmonella in India. Understanding these trends is important in planning future approaches to therapy, which serve as a baseline for assessment of the impact of new typhoid conjugate vaccines against these resistant organisms.

Current antibiotic use in the treatment of enteric fever in children

Background & objectives

Antimicrobial resistance is a major challenge in the treatment of typhoid fever with limited choices left to empirically treat these patients. The present study was undertaken to determine the current practices of antibiotic use in children attending a tertiary care hospital in north India.

Methods

This was a descriptive observational study in children suffering from enteric fever as per the case definition including clinical and laboratory parameters. The antibiotic audit in hospitalized children was measured as days of therapy per 1000 patient days and in outpatient department (OPD) as antibiotic prescription on the treatment card.

Results

A total of 128 children with enteric fever were included in the study, of whom, 30 were hospitalized and 98 were treated from OPD. The mean duration of fever was 9.5 days at the time of presentation. Of these, 45 per cent were culture positive with Salmonella Typhi being aetiological agent in 68 per cent followed by S. Paratyphi A in 32 per cent. During hospitalization, the average length of stay was 10 days with mean duration of defervescence 6.4 days. Based on antimicrobial susceptibility ceftriaxone was given to 28 patients with mean duration of treatment being six days. An additional antibiotic was needed in six patients due to clinical non-response. In OPD, 79 patients were prescribed cefixime and additional antibiotic was needed in five during follow up visit.

Interpretation & conclusions

Based on our findings, ceftriaxone and cefixime seemed to be the first line of antibiotic treatment for typhoid fever. Despite susceptibility, clinical non-response was seen in around 10 per cent of the patients who needed combinations of antibiotics.

Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi

Objectives

Surveillance of antimicrobial resistance (AMR) in Salmonella enterica serovars Typhi and Paratyphi is essential to provide an evidence base for empirical treatment protocols and to monitor emerging AMR. We sought to compare phenotypic and WGS-based genotypic methods for the detection of AMR in Salmonella Typhi and Salmonella Paratyphi.

Methods

WGS data from 603 isolates of Salmonella Typhi (n = 332) and Salmonella Paratyphi (n = 271) were mapped to genes or chromosomal mutations known to be associated with phenotypic AMR and compared with phenotypic susceptibility data interpreted using breakpoints recommended by EUCAST.

Results

There were two (0.03%) discordant interpretations out of a possible 6030 isolate/antimicrobial class combinations. MDR (resistant to three or more classes of antimicrobial) was detected in 83/332 (25.0%) Salmonella Typhi isolates, but was not detected in Salmonella Paratyphi. Thirty-six (10.8%) isolates of Salmonella Typhi were resistant to ciprofloxacin (MIC >0.5 mg/L), with 33 (9.9%) of 332 exhibiting mutations in gyrA and parC, and 244 (73.5%) isolates had reduced susceptibility to ciprofloxacin (MIC 0.06-0.25 mg/L). In comparison, 209/227 (92.1%) isolates of Salmonella Paratyphi A exhibited resistance to ciprofloxacin (MIC >0.5 mg/L). No resistance to azithromycin or the third-generation cephalosporins was detected.

Conclusions

WGS data provided a robust and informative approach for monitoring MDR and emerging resistance to ciprofloxacin in Salmonella Typhi and Salmonella Paratyphi. Phenotypic antimicrobial susceptibility testing continues to be performed to guide targeted individual patient treatment, but inferred AMR profiles from WGS data may be used for surveillance and to guide empirical therapy.

Changing trends of culture-positive typhoid fever and antimicrobial susceptibility in a tertiary care North Indian Hospital over the last decade

Purpose

The present study was undertaken to analyse the trend in prevalence of culture-positive typhoid fever during the last decade and to determine antimicrobial susceptibility profile of Salmonella Typhi and Salmonella Paratyphi A isolated from patients of enteric fever presenting to our hospital.

Methods

All the culture-positive enteric fever cases during 2005-2016 presenting to our Hospital were included in the study. Antimicrobial susceptibility was done against chloramphenicol, amoxicillin, co-trimoxazole, ciprofloxacin, ofloxacin, levofloxacin, pefloxacin, ceftriaxone and azithromycin as per corresponding CLSI guidelines for each year. We also analysed the proportion of culture positivity during 1993-2016 in light of the antibiotic consumption data from published literature.

Results

A total of 1066 strains-S. Typhi (772) and S. Paratyphi A (294) were isolated from the blood cultures during the study. A maximum number of cases were found in July-September. Antimicrobial susceptibility for chloramphenicol, amoxicillin and co-trimoxazole was found to be 87.9%, 75.5%, 87.3% for S. Typhi and 94.2%, 90.1% and 94.2% for S. Paratyphi A, respectively. Ciprofloxacin, ofloxacin and levofloxacin susceptibility were 71.3%, 70.8% and 70.9% for S. Typhi and 58.1%, 57.4% and 57.1% for S. Paratyphi A, respectively. Azithromycin susceptibility was 98.9% in S. Typhi. Although susceptibility to ceftriaxone and cefixime was 100% in our isolates, there is a continuous increase in ceftriaxone minimum inhibitory concentration (MIC)₅₀and MIC₉₀values over the time. The proportion of blood culture-positive cases during 1993-2016 ranged from a minimum of 0.0006 in 2014 to a maximum of 0.0087 in 1999.

Conclusion

We found that the most common etiological agent of enteric fever is S. Typhi causing the majority of cases from July to October in our region. MIC to ceftriaxone in typhoidal salmonellae is creeping towards resistance and more data are needed to understand the azithromycin susceptibility.

Pefloxacin as a surrogate marker for quinolone susceptibility in Salmonella enterica serovars Typhi & Paratyphi A in India

Background & objectives:

The emergence of resistance to fluoroquinolones in enteric fever despite the pathogen being susceptible by in vitro laboratory results, led to repeated changes in Clinical and Laboratory Standard Institute (CLSI) guidelines for this class of antibiotics to have specific and sensitive interpretative criteria. In 2015, CLSI added pefloxacin disk diffusion criteria as a surrogate marker for fluoroquinolone susceptibility. This study was carried out to evaluate the use of pefloxacin as a surrogate marker for ciprofloxacin, ofloxacin and levofloxacin susceptibility in clinical isolates of Salmonella Typhi and S. Paratyphi A.

Methods:

A total of 412 strains of S. Typhi and S. Paratyphi A were studied for pefloxacin disk diffusion test as a surrogate marker for susceptibility to ciprofloxacin, ofloxacin and levofloxacin as per CLSI and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Molecular mechanisms of resistance to fluoroquinolones were also determined and correlated with pefloxacin susceptibility breakpoints.

Results:

Of the total 412 strains, 34 were susceptible to ciprofloxacin and 33 each to levofloxacin and ofloxacin using CLSI minimum inhibitory concentration (MIC) breakpoints. There was a positive correlation between MICs with correlation coefficients 0.917, 0.896 and 0.958 for the association between ciprofloxacin and ofloxacin, ciprofloxacin and levofloxacin and ofloxacin and levofloxacin, respectively (P <0.001). The sensitivity, specificity and positive predictive value of pefloxacin as a surrogate marker using ciprofloxacin MIC as a gold standard were 100, 99.5 and 94.4 per cent, while 100, 99.2 and 91.7 per cent taking ofloxacin and levofloxacin MIC as gold standard. Mutations in target genes correlated with the pefloxacin susceptibility results.

Interpretation & conclusions:

Our results showed that pefloxacin served as a good surrogate marker for the detection of susceptibility to ciprofloxacin, ofloxacin and levofloxacin in S. Typhi and S. Paratyphi A. Further studies are required to confirm these findings.

Characterization of antimicrobial resistance markers & their stability in Salmonella enterica serovar Typhi

Background & objectives:

Typhoid fever is a major cause of morbidity and mortality in the developing countries including India. Resistance to multiple antimicrobial agents is an emerging global problem that has serious impact on the treatment of disease. There are many factors associated with the emergence of resistance. Most important of them is the acquisition and further transmission and spread of resistance markers among various bacterial species. Therefore, we conducted this study to characterize the resistance plasmids in terms of their transferability and stability among Salmonellaenterica serovar Typhi.

Methods:

Six multidrug-resistant S. Typhi isolates were evaluated for the stability and transfer of resistance markers. The resistance plasmids were also checked for the presence of RepHI1A replicon.

Results:

All resistance markers were found to be transferred to the recipient through conjugation and transformation, except for nalidixic acid. None of the resistance plasmid was found to harbour RepHI1A replicon and therefore, did not belong to incompatibility group IncHI1. Resistance markers were found to be highly stable in all the isolates during serial passages and storage as stab cultures at different temperatures for different time periods.

Interpretation & conclusions:

Resistance markers for chloramphenicol, ampicillin, streptomycin and trimethoprim were transferred through conjugation as well as transformation whereas that for nalidixic acid was not transferred in any of the isolates. Markers for chloramphenicol and streptomycin resistance were found to be most stable during various storage conditions. Presence of small-sized non-IncHI1 resistance plasmids is a matter of concern due to their capability to exist inside the host, thereby increasing the possibility of their transmission and spread among S. Typhi and other bacterial species.

Molecular Characterization of Intermediate Susceptible Typhoidal Salmonella to Ciprofloxacin, and its Impact

BACKGROUND AND OBJECTIVE

Extensive use of ciprofloxacin to treat Salmonella typhi infections has led to the emergence of resistance, resulting in clinical failure and delayed treatment response. Interpretative breakpoints for ciprofloxacin were revised by the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) in 2012. Since the majority of S. typhi isolates fall under the category of 'intermediate susceptible' as per CLSI criteria, we undertook molecular characterization to better define the susceptibility of these isolates.

METHODS

Of 113 typhoidal Salmonella isolates collected during 2014, 33 (27 S. typhi and 6 S. paratyphi A) were randomly selected to determine the presence of chromosomal (gyrA, gyrB and parC), plasmid (qnrA, qnrB, qnrS and aac(6')-lb-cr), and efflux-mediated fluoroquinolone resistance.

RESULTS

To the best of our knowledge, the parC mutation Glu(84)-Gly was observed for the first time in S. typhi in India. Of 33 isolates, only one harbored the qnrB gene, which is responsible for plasmid-mediated resistance. No significant change in efflux pump activity was observed for ciprofloxacin, except one that showed a fivefold decrease. Ninety-six percent of isolates with intermediate minimum inhibitory concentration to ciprofloxacin (CLSI) had mutations in the gyrA and parC genes, which might translate to possible/probable clinical failure in patients if treated with ciprofloxacin. In contrast, the EUCAST criteria define these isolates as resistant and may result in appropriate therapy with reduced morbidity.

CONCLUSION

It was clear that the molecular mechanism of ciprofloxacin resistance correlates better with the EUCAST criteria than the CLSI criteria, which is also in agreement with the pefloxacin results, suggesting it as a surrogate marker for identifying fluoroquinolone susceptibility.

Six-year susceptibility trends and effect of revised Clinical Laboratory Standards Institute breakpoints on ciprofloxacin susceptibility reporting in typhoidal Salmonellae in a tertiary care paediatric hospital in Northern India

The antimicrobial trends over 6 years were studied, and the effect of revised Clinical Laboratory Standards Institute (CLSI) breakpoints (2012) for ciprofloxacin susceptibility reporting in typhoidal Salmonellae was determined. A total of 874 (95.4%) isolates were nalidixic acid-resistant (NAR). Using the CLSI 2011 guidelines (M100-S21), 585 (66.9%) isolates were ciprofloxacin susceptible. The susceptibility reduced to 11 (1.25%) isolates when interpreted using 2012 guidelines (M100-S22). Among the forty nalidixic acid susceptible (NAS) Salmonellae, susceptibility to ciprofloxacin decreased from 37 isolates (M100-S21) to 12 isolates (M100-S22). The 25 cases which appeared resistant with newer guidelines had a minimum inhibitory concentration (MIC) range between 0.125 and 0.5 μg/ml. MIC50 for the third generation cephalosporins varied between 0.125 and 0.5 μg/ml over 6 years whereas MIC90 varied with a broader range of 0.19-1 μg/ml. The gap between NAR and ciprofloxacin-resistant strains identified using 2011 guidelines has been reduced; however, it remains to be seen whether additional NAS, ciprofloxacin-resistant isolates are truly resistant to ciprofloxacin by other mechanisms of resistance.

Typhoidal Salmonellae: Use of Multi-Locus Sequence Typing to Determine Population Structure

Enteric fever is an invasive infection predominantly caused by Salmonella enterica serovars Typhi and Paratyphi A. The pathogens have evolved from other nontyphoidal salmonellaeto become invasive and host restricted. Emergence of antimicrobial resistance in typhoidal salmonellae in some countries is a major therapeutic concern as the travelers returning from endemic countries carry resistant strains to non endemic areas. In order to understand the epidemiology and to design disease control strategies molecular typing of the pathogen is very important. We performed Multilocus Sequence Typing (MLST) of 251 S. Typhi and 18 S. Paratyphi strains isolated from enteric fever patients from seven centers across India during 2010-2013to determine the population structure and prevalence of MLST sequence types in India. MLST analysis revealed the presence of five sequence types (STs) of typhoidal salmonellae in India namely ST1, ST2 and ST3 for S. Typhi and ST85 and ST129 for S. Paratyphi A.S. Typhi strains showed monophyletic lineage and clustered in to 3 Sequence Types—ST1, ST2 and ST3 and S. Paratyphi A isolates segregated in two sequence types ST85 and ST129 respectively. No association was found between antimicrobial susceptibility and sequence types. This study found ST1 as the most prevalent sequence type of S. Typhi in India followed by ST2, which is in concordance with previous studies and MLST database. In addition a rare sequence type ST3 has been found which is reported for the first time from the Indian subcontinent. Amongst S. Paratyphi A, the most common sequence type is ST129 as also reported from other parts of world. This distribution and prevalence suggest the common spread of the sequence types across the globe and these findings can help in understanding the disease distribution.

GyrA ser83 and ParC trp106 Mutations in Salmonella enterica Serovar Typhi Isolated from Typhoid Fever Patients in Tertiary Care Hospital

INTRODUCTION

Typhoid fever is endemic in India and other developing countries, causing major public health problems with high morbidity and mortality. The resistance of Salmonella enterica serovar Typhi (S. Typhi) towards commonly prescribed antimicrobials is increasing in developing countries. However, there have been several reports of the therapeutic failure of fluoroquinolones in patients with Salmonella infection. Resistance to quinolones/ fluoroquinolones commonly arises due to target site mutation.

AIM

The present study was planned to analyze mutation in Quinolone Resistance Determining Region (QRDR) of quinolone resistant Salmonella isolates.

MATERIALS AND METHODS

A total of 133 S. Typhi isolates (blood (n = 131), stool (n=1) and bone marrow aspirate (n=1)) from tertiary care hospitals in Chennai and Puducherry, were included in this study. Minimum Inhibitory Concentrations (MIC) were carried out according to the Clinical Laboratory Standard Institute (CLSI)guidelines 2014. Mutations in gyrA and parC genes were analyzed by PCR-RFLP (Restriction Fragment Length Polymorphism) method followed by DNA sequencing.

RESULTS

Of the 133 S. Typhi, 99.2% were resistant to nalidixic acid and 21% were resistant to ciprofloxacin by MIC method. 94% of isolates showed Ser 83 mutation in gyrA and 21.8% of isolates showed Trp106-Gly mutation in parC.

CONCLUSION

Mutations in gyrA and parC genes are highly prevalent among Salmonella species. Irrational use of fluoroquinolones may increase the accumulation of mutations in the DNA gyrase and topoisomerase encoding genes, which lead to the emergence of high level fluoroquinolone-resistant Salmonella strains in future.

Attenuation of in vitro host-pathogen interactions in quinolone-resistant Salmonella Typhi mutants

OBJECTIVES

The relationship between quinolone resistance acquisition and invasion impairment has been studied in some Salmonella enterica serovars. However, little information has been reported regarding the invasive human-restricted pathogen Salmonella Typhi. The aim of this study was to investigate the molecular mechanisms of quinolone resistance acquisition and its impact on virulence in this serovar.

METHODS

Two antibiotic-resistant mutants (Ty_c1 and Ty_c2) were generated from a Salmonella Typhi clinical isolate (Ty_wt). The three strains were compared in terms of antimicrobial susceptibility, molecular mechanisms of resistance, gene expression of virulence-related factors, ability to invade eukaryotic cells (human epithelial cells and macrophages) and cytokine production.

RESULTS

Multidrug resistance in Ty_c2 was attributed to AcrAB/TolC overproduction, decreased OmpF (both mediated by the mar regulon) and decreased OmpC. The two mutants showed a gradually reduced expression of virulence-related genes (invA, hilA, hilD, fliC and fimA), correlating with decreased motility, reduced infection of HeLa cells and impaired uptake by and intracellular survival in human macrophages. Moreover, Ty_c2 also showed reduced tviA expression. Additionally, we revealed a significant reduction in TNF-α and IL-1β production and decreased NF-κB activation.

CONCLUSIONS

In this study, we provide an in-depth characterization of the molecular mechanisms of antibiotic resistance in the Salmonella Typhi serovar and evidence that acquisition of antimicrobial resistance is concomitantly detected with a loss of virulence (epithelial cell invasion, macrophage phagocytosis and cytokine production). We suggest that the low prevalence of clinical isolates of Salmonella Typhi highly resistant to ciprofloxacin is due to poor immunogenicity and impaired dissemination ability of these isolates.

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.

Renal Abscess Caused by Salmonella Typhi

Salmonella typhi is a true pathogen, which is capable of causing both intestinal and extraintestinal infections. Unusual presentations of Salmonella should always be kept in mind as this organism can cause disease in almost any organ of the body. S. typhi has been reported to cause the life-threatening infections such as meningitis, endocarditis, myocarditis, empyema, and hepatic abscess. Renal involvement by S. typhi is a relatively rare presentation. We report a case of renal abscess caused by S. typhi in an afebrile, 10-year-old child who did not have any clinical history of enteric fever. To our knowledge, this is the first reported case of isolation of S. typhi from the renal abscess, and interestingly this isolate was found to be resistant to quinolones.

Study of the role of efflux pump in ciprofloxacin resistance in Salmonella enterica serotype Typhi

PURPOSE

There are increasing reports on failure of clinical response to ciprofloxacin in typhoid fever despite the strain being sensitive to drug in in-vitro using standard guidelines and showing mutations in DNA gyrase. But this increased MIC and clinical failures with ciprofloxacin are not always co-related with mutations presently identified in gyrA and parC genes. This shows that there may be other mechanisms such as an active drug efflux pump responsible as has been shown in other Enterobacteriaceae. This study was carried out to determine the role of efflux pump in Salmonella Typhi isolates.

MATERIALS AND METHODS

Total 25 already characterized nalidixic acid sensitive and nalidixic acid resistant S. Typhi strains with different range of ciprofloxacin MIC were included to study the role of efflux pump in the presence of CCCP (efflux pump inhibitor). For genotypic characterization, the entire acrR gene was sequenced to confirm the presence of any mutation in the gene.

RESULTS

The MIC of ciprofloxacin remained same in the presence and absence of CCCP in the studied strains and no significant mutations were found in the acrR gene in any of the isolates studied.

CONCLUSIONS

No role of efflux pump in ciprofloxacin resistance was found in strains studied. There is a need to explore further mechanism of ciprofloxacin resistance in Salmonella Typhi.

Structure based in silico analysis of quinolone resistance in clinical isolates of Salmonella Typhi from India

Enteric fever is a major cause of morbidity in several parts of the Indian subcontinent. The treatment for typhoid fever majorly includes the fluoroquinolone group of antibiotics. Excessive and indiscriminate use of these antibiotics has led to development of acquired resistance in the causative organism Salmonella Typhi. The resistance towards fluoroquinolones is associated with mutations in the target gene of DNA Gyrase. We have estimated the Minimum Inhibitory Concentration (MIC) of commonly used fluoroquinolone representatives from three generations, ciprofloxacin, ofloxacin, levofloxacin and moxifloxacin, for 100 clinical isolates of Salmonella Typhi from patients in the Indian subcontinent. The MICs have been found to be in the range of 0.032 to 8 μg/ml. The gene encoding DNA Gyrase was subsequently sequenced and point mutations were observed in DNA Gyrase in the quinolone resistance determining region comprising Ser83Phe/Tyr and Asp87Tyr/Gly. The binding ability of these four fluoroquinolones in the quinolone binding pocket of wild type as well as mutant DNA Gyrase was computationally analyzed by molecular docking to assess their differential binding behaviour. This study has revealed that mutations in DNA Gyrase alter the characteristics of the binding pocket resulting in the loss of crucial molecular interactions and consequently decrease the binding affinity of fluoroquinolones with the target protein. The present study assists in understanding the underlying molecular and structural mechanism for decreased fluoroquinolone susceptibility in clinical isolates as a consequence of mutations in DNA Gyrase.

Determination of antimicrobial resistance in Salmonella spp

Infections with Salmonella are an important public health problem worldwide. Salmonella are one of the most common causes of food-borne illness in humans. There are many types of Salmonella but they can be divided into two broad categories: those that cause typhoid and those that do not. The typhoidal Salmonella (TS), such as S. enterica subsp. enterica serovars Typhi and S. Paratyphi only colonize humans and are usually acquired by the consumption of food or water contaminated with human fecal material. The much broader group of non-typhoidal Salmonella (NTS) usually results from improperly handled food that has been contaminated by animal or human fecal material. Antimicrobials are critical to the successful outcome of invasive Salmonella infections and enteric fever. Due to resistance to the older antimicrobials, ciprofloxacin [fluoroquinolone (FQ)] has become the first-line drug for treatment. Nevertheless, switch to FQ has led to a subsequent increase in the occurrence of salmonellae resistant to this antimicrobial agent. The exact mechanism of this FQ resistance is not fully understood. FQ resistance has driven the use of third-generation cephalosporins and azithromycin. However, there are sporadic worldwide reports of high level resistance to expanded-spectrum cephalosporins (such as ceftriaxone) in TS and in NTS it has been recognized since 1988 and are increasing in prevalence worldwide. Already there are rare reports of azithromycin resistance leading to treatment failure. Spread of such resistance would further greatly limit the available therapeutic options, and leave us with only the reserve antimicrobials such as carbapenem and tigecycline as possible treatment options. Here, we describe the methods involved in the genotypic characterization of antimicrobial resistance in clinical isolates of salmonellae.

Gatifloxacin versus ofloxacin for the treatment of uncomplicated enteric fever in Nepal: an open-label, randomized, controlled trial

Background

Fluoroquinolones are the most commonly used group of antimicrobials for the treatment of enteric fever, but no direct comparison between two fluoroquinolones has been performed in a large randomised trial. An open-label randomized trial was conducted to investigate whether gatifloxacin is more effective than ofloxacin in the treatment of uncomplicated enteric fever caused by nalidixic acid-resistant Salmonella enterica serovars Typhi and Paratyphi A.

Methodology and Principal Findings

Adults and children clinically diagnosed with uncomplicated enteric fever were enrolled in the study to receive gatifloxacin (10 mg/kg/day) in a single dose or ofloxacin (20 mg/kg/day) in two divided doses for 7 days. Patients were followed for six months. The primary outcome was treatment failure in patients infected with nalidixic acid resistant isolates. 627 patients with a median age of 17 (IQR 9–23) years were randomised. Of the 218 patients with culture confirmed enteric fever, 170 patients were infected with nalidixic acid-resistant isolates. In the ofloxacin group, 6 out of 83 patients had treatment failure compared to 5 out of 87 in the gatifloxacin group (hazard ratio [HR] of time to failure 0.81, 95% CI 0.25 to 2.65, p = 0.73). The median time to fever clearance was 4.70 days (IQR 2.98–5.90) in the ofloxacin group versus 3.31 days (IQR 2.29–4.75) in the gatifloxacin group (HR = 1.59, 95% CI 1.16 to 2.18, p = 0.004). The results in all blood culture-confirmed patients and all randomized patients were comparable.

Conclusion

Gatifloxacin was not superior to ofloxacin in preventing failure, but use of gatifloxacin did result in more prompt fever clearance time compared to ofloxacin. Trial registration: ISRCTN 63006567 (www.controlled-trials.com).

Enteric fever, which comprises of typhoid and paratyphoid fevers, is common in many developing countries. It is also sometimes seen in the Western world in returning travellers. This present study of uncomplicated enteric fever in an outpatient setting in a hospital in Kathmandu, Nepal compared the newer gatifloxacin with the widely-used ofloxacin (two drugs of the fluroquinolone class) in the treatment of this illness. Although fluroquinolones are commonly considered the main group of drugs in the treatment of enteric fever, there have not been comparisons of efficacy between two drugs in this same class in the treatment of enteric fever. Furthermore, certain strains of enteric fever organism called nalidixic-acid resistant strains are proving very difficult to treat in both the local population and the Western travellers. The study focused primarily on the efficacy of the 2 drugs against these particular strains. The results revealed that both drugs were effective but gatifloxacin decreased the patient's fever more rapidly than ofloxacin. Dysglycemia was noted in a 35-year-old woman taking gatifloxacin who did not disclose a pre-existing diagnosis of diabetes at time of enrollment, but not in any other healthy child or young adult.

Bloodstream infection among children presenting to a general hospital outpatient clinic in urban Nepal

Background

There are limited data on the etiology and characteristics of bloodstream infections in children presenting in hospital outpatient settings in South Asia. Previous studies in Nepal have highlighted the importance of murine typhus as a cause of febrile illness in adults and enteric fever as a leading bacterial cause of fever among children admitted to hospital.

Methods

We prospectively studied a total of 1084 febrile children aged between 2 months and 14 years presenting to a general hospital outpatient department in Kathmandu Valley, Nepal, over two study periods (summer and winter). Blood from all patients was tested by conventional culture and by real-time PCR for Rickettsia typhi.

Results

Putative etiological agents for fever were identified in 164 (15%) patients. Salmonella enterica serovar Typhi (S. Typhi) was identified in 107 (10%), S. enterica serovar Paratyphi A (S. Paratyphi) in 30 (3%), Streptococcus pneumoniae in 6 (0.6%), S. enterica serovar Typhimurium in 2 (0.2%), Haemophilus influenzae type b in 1 (0.1%), and Escherichia coli in 1 (0.1%) patient. S. Typhi was the most common organism isolated from blood during both summer and winter. Twenty-two (2%) patients were PCR positive for R. typhi. No significant demographic, clinical and laboratory features distinguished culture positive enteric fever and murine typhus.

Conclusions

Salmonella infections are the leading cause of bloodstream infection among pediatric outpatients with fever in Kathmandu Valley. Extension of immunization programs against invasive bacterial disease to include the agents of enteric fever and pneumococcus could improve the health of children in Nepal.

In vitro susceptibility testing of fluoroquinolone activity against Salmonella: recent changes to CLSI standards

Fluoroquinolone (FQ) resistance in Salmonella enterica is a significant clinical concern. Recognition of resistance by the clinical laboratory is complicated by the multiple FQ resistance mechanisms found in Salmonella. The Clinical Laboratory Standards Institute (CLSI) recently addressed this issue by revising the ciprofloxacin break points for Salmonella species. It is critical for clinicians and laboratory workers to be aware of the multiple technical issues surrounding these revised break points. In this article, we review FQ resistance mechanisms in Salmonella, their clinical significance, and data supporting the revised ciprofloxacin break points. We encourage clinical laboratories to adopt the revised CLSI ciprofloxacin break points for all Salmonella isolates in which susceptibility testing is indicated and discuss the technical issues for laboratories using commercial antimicrobial susceptibility systems.

Antimicrobial resistance trends in blood culture positive Salmonella Typhi isolates from Pondicherry, India, 2005-2009

Typhoid fever is caused by Salmonella enterica serovar Typhi, a major public health concern in developing countries. Recently, there has been an upsurge in the occurrence of bacterial isolates that are resistant to ciprofloxacin, and the emergence of broad spectrum β-lactamases in typhoidal salmonellae constitutes a new challenge for the clinician. A total of 337 blood culture isolates of S. Typhi, isolated from Pondicherry, India, between January 2005 and December 2009, were investigated using phenotypic, molecular and serological methods. Of the 337 isolates, 74 (22%) were found to be multidrug resistant (MDR) and 264 (78%) nalidixic acid resistant (NAR). Isolates with reduced susceptibility to ciprofloxacin possessed single mutations in the gyrA gene. A high rate of resistance (8%) was found to ciprofloxacin. All isolates with a ciprofloxacin MIC ≥ 4 mg/L possessed both double mutations in the QRDR of the gyrA gene and a single mutation in the parC gene. Active efflux pump mechanisms were also found to be involved in ciprofloxacin resistance. Finally, a large number of PFGE patterns (non-clonal genotypes) were observed among the S. Typhi isolates. In conclusion, a high rate of ciprofloxacin resistance was observed in comparison to other endemic areas in blood culture isolates of S. Typhi from Pondicherry, India, with steadily increasing NAR but decreasing MDR isolations over the study period. This is most likely to be due to an increased use of ciprofloxacin as a first-line drug of choice over more traditional antimicrobial agents for the treatment of typhoid fever.

The influence of reduced susceptibility to fluoroquinolones in Salmonella enterica serovar Typhi on the clinical response to ofloxacin therapy

Background

Infection with Salmonella enterica serovar Typhi (S. Typhi) with reduced susceptibility to fluoroquinolones has been associated with fluoroquinolone treatment failure. We studied the relationship between ofloxacin treatment response and the ofloxacin minimum inhibitory concentration (MIC) of the infecting isolate. Individual patient data from seven randomised controlled trials of antimicrobial treatment in enteric fever conducted in Vietnam in which ofloxacin was used in at least one of the treatment arms was studied. Data from 540 patients randomised to ofloxacin treatment was analysed to identify an MIC of the infecting organism associated with treatment failure.

Principal Findings

The proportion of patients failing ofloxacin treatment was significantly higher in patients infected with S. Typhi isolates with an MIC≥0.25 µg/mL compared with those infections with an MIC of ≤0.125 µg/mL (p<0.001). Treatment success was 96% when the ofloxacin MIC was ≤0.125 µg/mL, 73% when the MIC was between 0.25 and 0.50 µg/mL and 53% when the MIC was 1.00 µg/mL. This was despite a longer duration of treatment at a higher dosage in patients infected with isolates with an MIC≥0.25 µg/mL compared with those infections with an MIC of ≤0.125 µg/mL.

Significance

There is a clear relationship between ofloxacin susceptibility and clinical outcome in ofloxacin treated patients with enteric fever. An ofloxacin MIC of ≥0.25 µg/mL, or the presence of nalidixic acid resistance, can be used to define S. Typhi infections in which the response to ofloxacin may be impaired.

Typhoid fever is an infection of the bloodstream caused by the organism Salmonella Typhi (S. Typhi). Treatment with antimicrobials is critical for preventing severe infection and even death, yet antimicrobial resistant organisms have become a problem in many places where typhoid is common. Fluoroquinolones are a group of antimicrobials that are commonly used to treat typhoid, we analysed data from 540 enteric fever patients treated with ofloxacin (a fluoroquinolone) to identify a level of resistance (minimum inhibitory concentration (MIC)) from the infecting organism which is associated with treatment failure. The proportion of patients failing treatment was higher in those infected with a bacterium with an MIC≥0.25 µg/mL, compared with those infections with an MIC of ≤0.125 µg/mL. Treatment success was 96% when the ofloxacin MIC was ≤0.125 µg/mL, yet only 53% when the MIC was 1.00 µg/mL. Our data demonstrates that an S. Typhi bacterium with an ofloxacin MIC of ≥0.25 µg/mL correlates with a poor outcome when treated with this antimicrobial. Therefore, we propose an amendment in the current MIC guidelines for microbiology laboratories to aid clinicians treating typhoid and suggest the use of alternative therapy in these patients.

Detection of novel gyrA mutations in nalidixic acid-resistant isolates of Salmonella enterica from patients with diarrhoea

The aim of the current study was to detect mutations in the gyrA gene of quinolone-resistant Salmonella spp. isolates recovered in Tehran, Iran. Between April 2008 and September 2009, 174 Salmonella spp. were collected and assayed for quinolone resistance and detection of gyrA mutations. Isolates identified as Salmonella enterica were tested for susceptibility by the disk diffusion method. Polymerase chain reaction (PCR) amplification and sequencing of the gyrA gene segment encoding the quinolone resistance-determining region (QRDR) were performed for the nalidixic acid-resistant isolates. Amongst the 174 recovered Salmonella spp. isolates, 89 were resistant to nalidixic acid, of which 9 were resistant to enrofloxacin; 10 isolates had reduced susceptibility to nalidixic acid. None of the isolates were resistant to ciprofloxacin, but a single isolate showed reduced susceptibility. Twelve types of amino acid replacement were found in the QRDR region of GyrA, namely the previously described substitutions in positions 83 and 87 as well as five new substitutions Leu41-Pro, Arg47-Ser, Ser111-Thr, Ala118-Thr and Asp147-Gly. Double substitutions in both positions 83 and 87 were not identified. A Gly133-Glu substitution was identified in a single S. enterica serotype Typhi isolate.

Suitable disk antimicrobial susceptibility breakpoints defining Salmonella enterica serovar Typhi isolates with reduced susceptibility to fluoroquinolones

Infections with Salmonella enterica serovar Typhi isolates that have reduced susceptibility to ofloxacin (MIC ≥ 0.25 μg/ml) or ciprofloxacin (MIC ≥ 0.125 μg/ml) have been associated with a delayed response or clinical failure following treatment with these antimicrobials. These isolates are not detected as resistant using current disk susceptibility breakpoints. We examined 816 isolates of S. Typhi from seven Asian countries. Screening for nalidixic acid resistance (MIC ≥ 16 μg/ml) identified isolates with an ofloxacin MIC of ≥0.25 μg/ml with a sensitivity of 97.3% (253/260) and specificity of 99.3% (552/556). For isolates with a ciprofloxacin MIC of ≥0.125 μg/ml, the sensitivity was 92.9% (248/267) and specificity was 98.4% (540/549). A zone of inhibition of ≤28 mm around a 5-μg ofloxacin disc detected strains with an ofloxacin MIC of ≥0.25 μg/ml with a sensitivity of 94.6% (246/260) and specificity of 94.2% (524/556). A zone of inhibition of ≤30 mm detected isolates with a ciprofloxacin MIC of ≥0.125 μg/ml with a sensitivity of 94.0% (251/267) and specificity of 94.2% (517/549). An ofloxacin MIC of ≥0.25 μg/ml and a ciprofloxacin MIC of ≥0.125 μg/ml detected 74.5% (341/460) of isolates with an identified quinolone resistance-inducing mutation and 81.5% (331/406) of the most common mutant (carrying a serine-to-phenylalanine mutation at codon 83 in the gyrA gene). Screening for nalidixic acid resistance or ciprofloxacin and ofloxacin disk inhibition zone are suitable for detecting S. Typhi isolates with reduced fluoroquinolone susceptibility.

Molecular characterization of antimicrobial resistance in non-typhoidal salmonellae associated with systemic manifestations from India

Extended-spectrum cephalosporins and fluoroquinolones are essential antimicrobials for treating invasive salmonellosis, although emerging resistance to these antimicrobials is of growing concern, especially in India. Therefore, a study was conducted to characterize the antimicrobial susceptibility phenotypes, types of extended-spectrum β-lactamase (ESBL) gene plasmids and serological relationships of 21 non-typhoidal Salmonella isolates from patients who attended three different hospitals in India from 2006 to 2008. The isolates were cultured from stool, blood and cerebrospinal fluid samples obtained from patients presenting with diarrhoea and accompanying systemic manifestations such as fever, vomiting and meningism. Non-typhoidal Salmonella isolates were investigated using serotyping and antimicrobial susceptibility testing. PCR screening was also performed to detect the β-lactamase, qnr and aac(6′)-Ib-cr genes and class 1 integrons. Sequencing for quinolone resistance mutations and plasmid replicon typing were also performed. An antimicrobial resistance microarray was used for preliminary screening and identification of bla TEM and bla SHV genes, and phenotypic testing for the presence of efflux pumps was also performed. Ten out of 21 isolates (48 %) possessed the extended-spectrum cephalosporin resistance phenotype, with PCR amplification and sequencing revealing that isolates possessed TEM-1, SHV-12, DHA-1, OXA-1-like and CTX-M-15 ESBL genes. FIIs plasmid replicons were detected in seven isolates (33 %). The involvement of efflux pumps was detected in four isolates (19 %) resistant to ciprofloxacin. It was concluded that SHV-12-carrying Salmonella serotype Agona may play an important role in ESBL-mediated resistance in non-typhoidal salmonellae in India. The very high percentage (48 %) of ESBL-producing non-typhoidal salmonellae isolated from these patients represents a real and immediate challenge to the effective antimicrobial therapy of Salmonella infections associated with systemic manifestations. Continued surveillance for the presence of ESBL-producing (non-typhoidal) salmonellae in India is essential.

Enteric fever in a 6-year-old traveler caused by Salmonella enterica serotypes Typhi and Paratyphi A: laboratory detection strategies and treatment options

We report the first pediatric case of enteric fever caused by Salmonella enterica serotypes Typhi and Paratyphi A. Mixed infections are infrequently reported, potentially because detection of two different Salmonella serotypes in blood cultures is technically challenging. We suggest laboratory strategies to aid in the recognition of mixed infections.

Increasing rates and clinical consequences of nalidixic acid-resistant isolates causing enteric fever in returned travellers: an 18-year experience

The purpose of this study was to examine the rate and clinical consequences of nalidixic acid-resistant (NAR) isolates in travellers with enteric fever presenting to a hospital in a developed country. We retrospectively examined microbiologically confirmed cases of enteric fever in adult returned travellers over an 18-year period presenting to two tertiary referral hospitals in Melbourne, Australia. There were 59 cases of Salmonella typhi infection, 43 cases of S. paratyphi A infection and two cases of S. paratyphi B infection. Most patients reported recent travel to India (36%) or Indonesia (29%). NAR isolates were commonly encountered (41% of all isolates), particularly from India (75%), Pakistan (80%) and Bangladesh (60%). The number of NAR isolates increased progressively after 2003. Patients with NAR isolates had prolonged mean fever clearance time (5.6 vs. 3.3 days, P = 0.03) and prolonged hospital stay (7.9 vs. 5.7 days, P = 0.02) compared to non-resistant isolates. This represents the largest report of NAR enteric fever in returned travellers. NAR isolates predominate in cases of enteric fever from South Asia and result in prolonged fever clearance time and hospital stay. Empiric therapy with alternative antibiotics such as ceftriaxone or azithromycin should be considered in patients with suspected enteric fever from this region.

Clonal expansion and microevolution of quinolone-resistant Salmonella enterica serotype typhi in Vietnam from 1996 to 2004

Salmonella enterica serotype Typhi clinical isolates (n = 91) resistant to nalidixic acid (Nal(r)) were collected from sporadic cases and minor outbreaks throughout Vietnam between 1996 and 2004. These isolates were typed and compared by four methods: Vi phage typing, PstI ribotyping, XbaI and SpeI pulsed-field gel electrophoresis (PFGE), and single-nucleotide polymorphism (SNP) analysis. The results indicated that 65% of the isolates were not typeable by Vi phage typing. In contrast, the ribotyping and, with more accuracy, the SNP analysis methods indicated that all Nal(r) isolates belonged to a single clone (ribotype 3a, haplotype H58) that was found previously and that largely consisted of plasmid-encoded multidrug-resistant serotype Typhi isolates. PFGE demonstrated the occurrence of microevolution within this clone. We identified two major combined PFGE profiles: X1-S1 and X3-S6. X3-S6 predominated between 1996 and 2002 but was replaced by X1-S1 after 2002. Nevertheless, PFGE, with a Simpson's index of 0.78, was not considered an optimal discriminatory method for investigating typhoid fever outbreaks in Vietnam. The rate of quinolone resistance increased and the rate of multidrug resistance decreased during the study period. From 2002 to 2004, 80.6% of the isolates from South Vietnam were resistant only to Nal. The mechanism of Nal resistance in most of the isolates (94%) was a mutation in the quinolone resistance-determining chromosomal region of gyrA that led to the amino acid substitution Ser83Phe. No plasmid-located qnrA, qnrB, or qnrS was detected.

Paratyphoid sepsis

A large for gestational age male baby was born to a healthy young primigravida, on L-thyroxime, at 40 weeks by caesarean delivery in a tertiary care hospital. The baby had episodes of hypoglycemia during his immediate four postnatal days in the nursery that were successfully managed with intravenous glucose administration. The baby became unwell on day 5 and had a positive sepsis-screening test. Blood culture revealed a multidrug susceptible S. Paratyphi A strain, which he probably acquired on the first or second postnatal day from the contaminated expressed breast milk or the formula feed.

Ciprofloxacin therapy for typhoid fever needs reconsideration

Outbreaks of multidrug-resistant Salmonella enterica serotype Typhi in the Indian subcontinent in the late 1980s resulted in the failure of conventional drugs, and ciprofloxacin became the firstline drug to treat enteric fever. However, reduced susceptibility to ciprofloxacin, reported widely since 1994, has posed a therapeutic difficulty. The aim of the present work was to review the situation of drug resistance among S. enterica serotype Typhi in central India from 1988 to 2005. A minimum inhibitory concentration (MIC) study for ciprofloxacin was carried out by the agar dilution method on 314 stock cultures preserved since 1988. The MIC for ciprofloxacin was < or = 0.125 mg/l for the 50 isolates isolated during 1989-1994, but during 1998-1999, 60% of the 50 isolates showed MIC > 0.125 mg/l, while in 2002-2003, 82.5 % of the 97 isolates had MIC > 0.125 mg/l and 35% had MIC > 1 mg/l (high-level resistance). In 2004-2005, 88.2% of the 77 isolates had MIC > 0.125 mg/l and 15% had MIC > 1 mg/l (high-level resistance). Sixty-four isolates showing MIC > 1 mg/l with the agar dilution method were also checked by Epsilometer test (E-test, AB Biodisk, Solna, Sweden). Based on the data, it is suggested to withdraw ciprofloxacin as a therapeutic agent for enteric fever. Fortunately, multiple drug resistance, with concurrent resistance to chloramphenicol, cotrimoxazole, and ampicillin, which had reached more than 90% in 1990-1991, started declining over the years and was as low as 5.6% in 2004-2005. According to these observations, older drugs such as chloramphenicol, cotrimoxazole, and ampicillin could be recalled to treat enteric fever.

Deep-seated resistance in relapsed paratyphoid fever

We describe a case of relapsed paratyphoid fever in which the isolate had reduced susceptibility to ciprofloxacin due to a rare mutation within the gyrA gene. 18fluorodeoxyglucose positron emission tomography scanning identified deep-seated infection including unsuspected aortitis and highlights the utility of novel imaging techniques to improve our understanding and treatment of this disease.

Antibiogram pattern and seasonality of Salmonella serotypes in a North Indian tertiary care hospital

The antibiogram pattern and seasonal distribution of Salmonella serotypes were analysed retrospectively over a 6-year period from January 1999 to December 2004. Blood cultures received in the Bacteriology Laboratory were processed by standard procedures and the Salmonella spp. isolates were identified with specific antisera and standard biochemical tests. Antimicrobial susceptibility testing was carried out by a standard disc diffusion method and the minimum inhibitory concentration (MIC) of ciprofloxacin for 332 representative Salmonella isolates was determined by E test. Salmonella Typhi (75.7%) was the predominant serotype among 830 Salmonella spp. isolated during the study period followed by S. Paratyphi A (23.8%). The maximum number of enteric fever cases occurred during April-June (dry season) followed by July-September (monsoon season). There was a decrease in multidrug-resistant (MDR) S. Typhi, but MDR S. Paratyphi A isolates increased. There was also a dramatic increase in nalidixic acid-resistant isolates. All isolates were susceptible to third-generation cephalosporins and ciprofloxacin except one S. Typhi strain which demonstrated high-level ciprofloxacin resistance with a MIC of 16 mug/ml. A knowledge of the seasonal distribution and antibiotic resistance pattern of Salmonella in a particular geographical region is helpful in the delineation of appropriate control measures required for prevention of enteric fever.

Analysis of Salmonella spp. with resistance to extended-spectrum cephalosporins and fluoroquinolones isolated in North America and Latin America: report from the SENTRY Antimicrobial Surveillance Program (1997–2004)

Emerging antimicrobial-resistant Salmonella spp. requires increased efforts to appropriately test susceptibility. The SENTRY Antimicrobial Surveillance Program monitored Salmonella spp. and detected nalidixic acid-resistant strains with elevated fluoroquinolone minimum inhibitory concentration (MIC) results and strains with extended-spectrum beta-lactamase (ESBL) "phenotypes" over the last 8 years. A total of 786 stool and bloodstream isolates from North American and Latin American medical centers (2001-2003) were tested by reference broth microdilution methods. Genetic analysis was used to further characterize the resistance mechanisms. Twenty-one sites forwarded 89 (11.3%) nalidixic acid-resistant (MIC, > or =32 microg/mL) strains. Nineteen of these isolates were studied to determine mutations in the quinolone resistance-determining region (QRDR). Among the nalidixic acid-resistant Salmonella spp. isolates, fluoroquinolone MIC values were also elevated (8- to 32-fold) compared with "wild-type" strains. Ciprofloxacin and gatifloxacin (MIC(90), 0.5 microg/mL) were more potent than levofloxacin and garenoxacin (1 microg/mL) against nalidixic acid-resistant strains. Single gyrA mutations were responsible for elevated fluoroquinolone MIC values and included D87Y (5), S83F (7), D87N (5), and S83Y (2). During 2001, 9 sites contributed 11 (2.9%) strains that met ESBL screening criteria (> or =2 microg/mL) for aztreonam or ceftazidime or ceftriaxone. ESBL confirmation was evaluated by Etest (AB BIODISK, Solna, Sweden) ESBL strips and the enzymes were characterized by polymerase chain reaction and gene sequencing. The ESBL phenotype isolates had the following MIC patterns: ceftazidime (> or =16 microg/mL), aztreonam (4 to >16 microg/mL), and ceftriaxone (8-32 microg/mL). All strains were susceptible to cefepime, carbapenems, gentamicin, and fluoroquinolones. No strains were inhibited by clavulanic acid consistent with all isolates producing the identified CMY-2, AmpC-like enzyme. Fluoroquinolones may be compromised among isolates with QRDR mutations detected using nalidixic acid as a screening agent. Salmonella spp. with ESBL phenotypes were likely to harbor CMY-2 (not an ESBL) and remain susceptible to cefepime, carbapenems, and fluoroquinolones, which can be used for serious invasive Salmonella spp. infections. Compared with the stool culture isolates, the blood culture isolates had higher QRDR mutations, but remained susceptible to the fluoroquinolones. The blood culture isolates were more susceptible to penicillins (ampicillin and ticarcillin) and not significantly different for ceftriaxone or trimethoprim/sulfamethoxazole susceptibility patterns. No QRDR trends over time were detected in North America, but increased resistance was observed in Latin America.

Typhoid and paratyphoid fever

Typhoid fever is estimated to have caused 21.6 million illnesses and 216,500 deaths globally in 2000, affecting all ages. There is also one case of paratyphoid fever for every four of typhoid. The global emergence of multidrug-resistant strains and of strains with reduced susceptibility to fluoroquinolones is of great concern. We discuss the occurrence of poor clinical response to fluoroquinolones despite disc sensitivity. Developments are being made in our understanding of the molecular pathogenesis, and genomic and proteomic studies reveal the possibility of new targets for diagnosis and treatment. Further, we review guidelines for use of diagnostic tests and for selection of antimicrobials in varying clinical situations. The importance of safe water, sanitation, and immunisation in the presence of increasing antibiotic resistance is paramount. Routine immunisation of school-age children with Vi or Ty21a vaccine is recommended for countries endemic for typhoid. Vi vaccine should be used for 2-5 year-old children in highly endemic settings.

Antimicrobial resistance in developing countries. Part I: recent trends and current status

The global problem of antimicrobial resistance is particularly pressing in developing countries, where the infectious disease burden is high and cost constraints prevent the widespread application of newer, more expensive agents. Gastrointestinal, respiratory, sexually transmitted, and nosocomial infections are leading causes of disease and death in the developing world, and management of all these conditions has been critically compromised by the appearance and rapid spread of resistance. In this first part of the review, we have summarised the present state of resistance in these infections from the available data. Even though surveillance of resistance in many developing countries is suboptimal, the general picture is one of accelerating rates of resistance spurred by antimicrobial misuse and shortfalls in infection control and public health. Reservoirs for resistance may be present in healthy human and animal populations. Considerable economic and health burdens emanate from bacterial resistance, and research is needed to accurately quantify the problem and propose and evaluate practicable solutions. In part II, to be published next month, we will review potential containment strategies that could address this burgeoning problem.

Clinical outcomes in typhoid fever: adverse impact of infection with nalidixic acid-resistant Salmonella typhi

BACKGROUND

Widespread use of fluoroquinolones has resulted in emergence of Salmonella typhi strains with decreased susceptibility to fluoroquinolones. These strains are identifiable by their nalidixic acid-resistance. We studied the impact of infection with nalidixic acid-resistant S. typhi (NARST) on clinical outcomes in patients with bacteriologically-confirmed typhoid fever.

METHODS

Clinical and laboratory features, fever clearance time and complications were prospectively studied in patients with blood culture-proven typhoid fever, treated at a tertiary care hospital in north India, during the period from November 2001 to October 2003. Susceptibility to amoxycillin, co-trimoxazole, chloramphenicol, ciprofloxacin and ceftriaxone were tested by disc diffusion method. Minimum inhibitory concentrations (MIC) of ciprofloxacin and ceftriaxone were determined by E-test method.

RESULTS

During a two-year period, 60 patients (age [mean +/- SD]: 15 +/- 9 years; males: 40 [67%]) were studied. All isolates were sensitive to ciprofloxacin and ceftriaxone by disc diffusion and MIC breakpoints. However, 11 patients had clinical failure of fluoroquinolone therapy. Infections with NARST isolates (47 [78%]) were significantly associated with longer duration of fever at presentation (median [IQR] 10 [7-15] vs. 4 [3-6] days; P = 0.000), higher frequency of hepatomegaly (57% vs. 15%; P = 0.021), higher levels of aspartate aminotransferase (121 [66-235] vs. 73 [44-119] IU/L; P = 0.033), and increased MIC of ciprofloxacin (0.37 +/- 0.21 vs. 0.17 +/- 0.14 microg/mL; P = 0.005), as compared to infections with nalidixic acid-susceptible isolates. All 11 patients with complications were infected with NARST isolates. Total duration of illness was significantly longer in patients who developed complications than in patients who did not (22 [14.8-32] vs. 12 [9.3-20.3] days; P = 0.011). Duration of prior antibiotic intake had a strong positive correlation with the duration of fever at presentation (r = 0.61; P = 0.000) as well as the total duration of illness (r = 0.53; P = 0.000).

CONCLUSION

Typhoid fever caused by NARST infection is associated with poor clinical outcomes, probably due to delay in initiating appropriate antibiotic therapy. Fluoroquinolone breakpoints for S. typhi need to be redefined and fluoroquinolones should no longer be used as first-line therapy, if the prevalence of NARST is high.