Emergence of Ciprofloxacin-Resistant Salmonella enterica Serovar Typhi in Italy

Uncovering the growing burden of enteric fever: A molecular analysis of Salmonella Typhi antimicrobial resistance

Enteric fever, a persistent public health challenge in developing regions, is exacerbated by suboptimal socioeconomic conditions, contaminated water and food sources, and insufficient sanitation. This study delves into the antimicrobial susceptibility of Salmonella Typhi, uncovering the genetic underpinnings of its resistance. Analyzing 897 suspected cases, we identified a significant prevalence of typhoid fever, predominantly in males (58.3 %) and younger demographics. Alarmingly, our data reveals an escalation in resistance to both primary and secondary antibiotics, with cases of multi-drug resistant (MDR) and extensively drug-resistant (XDR) S. Typhi reaching 14.7 % and 43.4 %, respectively, in 2021. The Multiple Antibiotic Resistance (MAR) index exceeded 0.2 in over half of the isolates, signaling widespread antibiotic misuse. The study discerned 47 unique antibiotic resistance patterns and pinpointed carbapenem and macrolide antibiotics as the remaining effective treatments against XDR strains, underlining the critical need to preserve these drugs for severe cases. Molecular examinations identified blaTEM, blaSHV, and blaCTX-M genes in ceftriaxone-resistant strains, while qnrS was specific to ciprofloxacin-resistant variants. Notably, all examined strains exhibited a singular mutation in the gyrA gene, maintaining wild-type gyrB and parC genes. The erm(B) gene emerged as the primary determinant of azithromycin resistance. Furthermore, a distressing increase in resistance genes was observed over three years, with erm(B), blaTEM and qnrS showing significant upward trends. These findings are a clarion call for robust antimicrobial stewardship programs to curtail inappropriate antibiotic use and forestall the burgeoning threat of antibiotic resistance in S. Typhi.

Antimicrobial Resistance of Salmonella Strains Isolated from Human, Wild Boar, and Environmental Samples in 2018-2020 in the Northwest of Italy

Antimicrobial resistance is one of the most challenging public health problems worldwide, and integrated surveillance is a key aspect in a One Health control strategy. Additionally, Salmonella is the second most common zoonosis in Europe. We aimed to investigate the circulation of Salmonella strains and their related antimicrobial resistance in human, environmental, and wild boar samples from the northwest of Italy, from 2018 to 2020, to obtain a more comprehensive epidemiological picture. Salmonella Typhimurium 1,4,[5],12:i:-, S. Veneziana and S. Newport were the most common serotypes occurring in humans, the environment, and wild boar, respectively. Antimicrobial resistance was rather common in Salmonella isolates, with those from human displaying the highest degree of resistance against sulfadiazine−sulfamerazine−sulfamethazine (>90% of resistance). Moreover, resistance against azithromycin were exclusively observed in environmental samples, while only 7.7% (95% CI = 1.6−20.8) of wild boar isolates experienced resistance against trimethoprim−sulfamethoxazole. Multidrug resistance concurrently involved up to seven antimicrobial classes in human isolates, including third-generation cephalosporins and fluoroquinolones. Salmonella Typhimurium in humans and serotypes Goldcoast and Rissen from environmental sources showed the highest levels of resistance. This study shows diverse antimicrobial resistance patterns in Salmonella strains isolated from different sources and gives a broad picture of antimicrobial resistance spread in wild animals, humans, and the environment.

Hotspots sequences of gyrA, gyrB, parC, and parE genes encoded for fluoroquinolones resistance from local Salmonella Typhi strains in Jakarta

Background

Infection of Salmonella enterica subsp. enterica serovar Typhi is the primary etiology of typhoid fever globally and is common in many developing countries, especially those with dense populations and poor environmental sanitation. Antibiotic fluoroquinolones were used for the treatment in the 1980s due to the resistance to the first-line antibiotics. However, many cases of treatment failure of fluoroquinolones in typhoidal patients have been reported from numerous countries in Asia, Europe, Africa, and America. Mutations in quinolone resistance determining regions (QRDR) genes, gyrA, gyrB, parC, and parE, are found in fluoroquinolone-resistant Salmonella Typhi. Contrast reports came from the S. Typhi isolates in Indonesia, mainly Jakarta and the surroundings, obtained from patients with typhoid fever, with good sensitivity to the fluoroquinolones, i.e., nalidixic acid, ciprofloxacin, moxifloxacin, and levofloxacin. The present study, therefore, aimed to identify the hotspot sequences of gyrA, gyrB, parC, and parE genes of the local S. Typhi strains based on their susceptibility to fluoroquinolones from patients with typhoid fever in Jakarta and its satellite cities.

Results

A total of 28 isolates were identified as S. Typhi. All isolates were susceptible to nalidixic acid, levofloxacin, and moxifloxacin. Twenty-seven isolates (96.4%) were susceptible to ciprofloxacin, with one isolate (3.6%) being intermediate. The hotspot sequences of gyrA, gyrB, parC, and parE genes from all isolates were identical to the fluoroquinolone-sensitive reference sequence Salmonella enterica subsp. enterica serovar Typhi Ty2 (NCBI GenBank AE014613.1), including the isolate with intermediate susceptibility. The mutation was not found, and amino acid deduced from all hotspots in susceptible and intermediate isolates showed no replacement in all reported codons.

Conclusions

This study showed that the local S. Typhi strains from Jakarta and surroundings were susceptible to fluoroquinolones (nalidixic acid, ciprofloxacin, levofloxacin, and moxifloxacin), and the hotspot sequences of the gyrA, gyrB, parC, and parE genes were all identical to the reference sequence. Thus, the hotspot sequences of the gyrA, gyrB, parC, and parE genes seemingly were conserved in Jakarta’s local S. Typhi strains and could be considered wild type. The phenotypic susceptibility was consistent with the genotypic characteristic without non-synonymous mutations associated with drug resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02666-z.

Prevalence of Antimicrobial Resistance Genes in Salmonella Typhi: A Systematic Review and Meta-Analysis

Salmonella enterica serovar Typhi (S. Typhi) that has developed resistance to many antimicrobials poses a serious challenge to public health. Hence, this study aimed to systematically determine the prevalence of antimicrobial resistance (AMR) in S. Typhi isolated from the environment and humans as well as to ascertain the spread of the selected AMR genes in S. Typhi. This systematic review and meta-analysis were performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines, and the study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO). A total of 2353 studies were retrieved from three databases, of which 42 studies fulfilled the selection criteria. The pooled prevalence of AMR S. Typhi (using a random-effect model) was estimated at 84.8% (95% CI; 77.3−90.2), with high heterogeneity (I2: 95.35%, p-value < 0.001). The high estimated prevalence indicates that control methods should be improved immediately to prevent the spread of AMR among S. Typhi internationally.

Antimicrobial susceptibility and genomic profiling of Salmonella enterica from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018–2019

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Salmonella enterica Typhi found to be most prevalent, with genetic diversity

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Low prevalence of invasive non-typhoidal Salmonella infections

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Salmonella enterica Typhimurium isolated, belonging to serotype 313

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High prevalence of multidrug-resistant strains

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Emergence of fluoroquinolone and cephalosporin resistance

Objectives

This study investigated antimicrobial susceptibility and genomic profiling of S. enterica isolated from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018–2019.

Method

This was a prospective hospital-based study involving routine blood culture samples submitted to the microbiology laboratory at the University Teaching Hospital. Identification of S. enterica and determination of antimicrobial susceptibility profiles was achieved through conventional and automated methods. Whole-genome sequencing (WGS) was conducted, and the sequence data outputs were processed for species identification, serotype determination, multilocus sequence typing (MLST) profile determination, identification of antimicrobial resistance determinants, and phylogeny.

Results

Seventy-six Salmonella enterica were isolated and 64 isolates underwent WGS. Salmonella Typhi (72%) was the most prevalent serotype. Notable was the occurrence of invasive non-typhoidal Salmonella Typhimurium ST313 (3%), resistance to cephalosporins (4%) and ciprofloxacin (5%), multidrug resistance (46%), and reduced susceptibility to ciprofloxacin (30%) and imipenem (3%). Phylogenetic cluster analysis showed multiple Salmonella serovars with a wide range of genetic diversity.

Conclusion

The genetic diversity of Salmonella Typhi, high prevalence of multidrug resistance, and the emergence of ciprofloxacin and cephalosporin resistance warrants improved hygiene and water and sanitation provision, continued surveillance to apprise antibiograms and inform policy, and the introduction of the typhoid conjugate vaccine.

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.

Extra-intestinal Salmonellosis in a Tertiary Care Center in Saudi Arabia

Introduction: Salmonella infection is one of the most common causes of gastroenteritis worldwide. It is associated with high morbidity and mortality if not treated properly. It has developed resistance to multiple antibiotics. These developments are concerning. This study sought to observe common patterns of invasive Salmonella infections, such as the common serotypes involved, presentation, sensitive investigations, and effective treatment. This study also aimed to examine the risk factors that can worsen the infection and increase morbidity and mortality. Methodology: This retrospective analysis included all patients who were diagnosed with invasive Salmonella infection at King Khalid University Hospital from May 2017 to December 2018. Most patients in this report were immunocompromised; however, a few previously healthy patients. Different types of specimens were collected. Twenty-two patients with invasive Salmonella were included in this study. Results: Sixteen of them had underlying conditions. The most common presenting symptoms of illness were fever (n = 13), vomiting (n = 6), and diarrhea (n = 4). Most blood samples (94%) were positive for Salmonella. All patients were discharged except three who died; these were all older patients with comorbidities. Although four different antimicrobial resistance patterns were noticed in this study, ciprofloxacin was the highest significant percentage (62.5%). Of five patients initially treated with ciprofloxacin, three of them expressed resistance to this antibiotic. Conclusion: The findings of this study support that immunocompromised patients and people with extreme ages are more likely to have serious medical illnesses and at higher risk of infection with Salmonella spp. Therefore, this study emphasises the importance of antimicrobial judicious utilisation. Tackling the escalating antibiotic resistance could be approached by implementing advanced public education levels to maintain high standards of food and water safety. Moreover, the urge to investigating newer drugs against Salmonella with an acceptable safety profile is a cornerstone to attenuate the rapidly acquired bacterial resistance precisely for those who are immunocompromised. Furthermore, predicting the mortality, morbidity and the clinical response is feasible according to the patient parameters and comorbidities.

Molecular mechanisms of antimicrobial resistance and phylogenetic relationships of Salmonella enterica isolates from febrile patients in Yangon, Myanmar

BACKGROUND

Enteric fever is common in southeast Asia. However, there is little information on the circulating Salmonella enterica strains causing enteric fever in Myanmar.

METHODS

We performed antimicrobial susceptibility testing and whole genome sequencing on S. enterica bloodstream isolates from febrile patients aged ≥12 y attending two hospitals in Yangon, Myanmar, from 5 October 2015 through 4 October 2016. We identified the serovar of S. enterica, determined antimicrobial susceptibility and the molecular mechanisms of resistance. We analysed phylogenetic relationships among Myanmar S. enterica isolates and those with isolates from neighbouring countries.

RESULTS

Of 73 S. enterica isolated, 39 (53%) were serovar Typhi and 34 (47%) were Paratyphi A. All isolates were susceptible to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole but resistant to ciprofloxacin. We identified mutations in chromosomal genes gyrA, gyrB and parC as responsible for fluoroquinolone resistance. All S. enterica Typhi isolates were of 4.3.1 subclade (formerly known as H58) and formed two closely related genotypic clusters; both clusters were most closely related to isolates from India from 2012. All S. enterica Paratyphi A were lineage C, clade C4 and were closely related.

CONCLUSION

Our study describes currently circulating S. enterica serovars in Myanmar, the genetic basis of their antimicrobial resistance and provides a genotypic framework for epidemiologic study.

Cephalosporin-resistant typhoid

Typhoid fever is endemic in developing countries like India. An increasing prevalence of resistance to cephalosporins and fluoroquinolones by Salmonella isolates is seen. We present an 8-month-old boy with invasive Salmonella typhi disease. Blood culture showed S. typhi sensitive to ampicillin–sulbactam and cotrimoxazole but resistant to fluoroquinolones and third-generation cephalosporins. Cerebrospinal fluid examination revealed an aseptic meningitic picture. He was treated with intravenous meropenem and azithromycin following which his condition improved. This case highlights the need for improvement in environment sanitation and hygiene combined with early vaccination against typhoid fever and antimicrobial stewardship to help reduce the emerging resistance to cephalosporins and fluoroquinolones.

Travel-Related Typhoid Fever: Narrative Review of the Scientific Literature

Enteric fever is a foodborne infectious disease caused by Salmonella enterica serotypes Typhi and Paratyphi A, B and C. The high incidence in low income countries can increase the risk of disease in travelers coming from high income countries. Pre-travel health advice on hygiene and sanitation practices and vaccines can significantly reduce the risk of acquiring infections. Although the majority of the cases are self-limiting, life-threatening complications can occur. Delayed diagnosis and cases of infections caused by multi-drug resistant strains can complicate the clinical management and affect the prognosis. More international efforts are needed to reduce the burden of disease in low income countries, indirectly reducing the risk of travelers in endemic settings. Surveillance activities can help monitor the epidemiology of cases caused by drug-susceptible and resistant strains.

Effect of sub-lethal chemical disinfection on the biofilm forming ability, resistance to antibiotics and expression of virulence genes of Salmonella Enteritidis biofilm-surviving cells

Although disinfection procedures are widely implemented in food environments, bacteria can survive and present increased virulence/resistance. Since little is known about these phenomena regarding biofilms, this study aimed to investigate the effect of chemical disinfection on biofilm-derived cells of Salmonella Enteritidis. Using a reference strain (NCTC 13349) and a food isolate (350), biofilm susceptibility to benzalkonium chloride (BAC), sodium hypochlorite (SH) and hydrogen peroxide (HP) was evaluated and biofilms were exposed to sub-lethal concentrations of each disinfectant. Biofilm-derived cells were characterized for their biofilm forming ability, antibiotic resistance and expression of virulence-associated genes. Except for a few instances, disinfectant exposure did not alter antibiotic susceptibility. However, SH and HP exposure enhanced the biofilm forming ability of Salmonella Enteritidis NCTC 13349. After BAC and HP exposure, biofilm-derived cells presented a down-regulation of rpoS. Exposure to BAC also revealed an up-regulation of invA, avrA and csgD on Salmonella Enteritidis NCTC 13349. The results obtained suggest that biofilm-derived cells that survive disinfection may represent an increased health risk.

Phytochemical Composition and Anti-Efflux Pump Activity of Hydroalcoholic, Aqueous, and Hexane Extracts of Artemisia tournefortiana in Ciprofloxacin-Resistant Strains of Salmonella enterica Serotype Enteritidis

BACKGROUND

The AcrB efflux pump in Salmonella species plays a significant role in the development of antibiotic resistance in ciprofloxacin-resistant Salmonella enteritidis. This study aimed to investigate the anti-efflux pump activity of Artemisia tournefortiana extracts among S. Enteritidis strains.

METHODS

The hydroalcoholic, aqueous, and hexanolic extracts of A. tournefortiana were prepared and phytochemical composition of extract was determined using gas chromatography/mass spectrometry (GC/MS) method. After antibiogram, the AcrB efflux pump was detected in ciprofloxacin intermediate and resistant S. enteritidis strains using cartwheel and Polymerase chain reaction (PCR) methods. Finally, minimum inhibitory concentrations (MIC) of extracts against S. enteritidis strains were evaluated. After treatment of S. enteritidis strains with sub-MIC concentrations of extracts, the expression level of AcrB efflux pump gene was evaluated using Real-Time PCR.

RESULTS

Phytochemical analysis of extracts using GC/MS method showed that hexadecanoic acid, ethyl ester (30.7%), and cyclopropane,1-(1-hydroxy-1-heptyl)-2-methylene-3-pentyl (17.8%) were the most dominant volatile components volatile compounds in the extract. The results of antibiogram, cartwheel and PCR methods showed that among 20 strains of S. enteritidis that were resistant and intermediate to ciprofloxacin, 16 strains had AcrB efflux pumps. Finally, Real-Time PCR results showed a significant down-regulation of acrB gene in S. enteritidis strains.

CONCLUSION

A. tournefortiana had anti-efflux activity and this plant can potentially be used as a natural efflux inhibitor for S. enteritidis strains.

Modulatory Effect of Lippia alba Essential Oil on the Activity of Clinically Used Antimicrobial Agents on Salmonella typhi and Shigella dysenteriae Biofilm

The essential oil obtained from the leaves of Lippia alba (Mill.) N.E. Brown (Verbenaceae) has shown great pharmacological potential as an analgesic, antispasmodic, and antimicrobial agent. The aim of this study was to evaluate the modulatory effect of Lippia alba essential oil (LaEO I) on the activity of clinically used antimicrobial agents on Salmonella enterica serovar Typhi (Salmonella typhi) and Shigella dysenteriae biofilms. The Minimum Inhibitory Concentration of LaEO I (MICLaEO I) was determined by the microdilution method, and the effect of LaEO I on the activity of clinically used antimicrobials was assessed by the Checkboard method. The values obtained from MICLaEO I and ciprofloxacin were used to evaluate the effect of time of exposure on cell viability. LaEO I main components were geranial (34.2%), neral (25.9%), and myrcene (12.5%). The MICLaEO I was 1 mg/mL for both strains. LaEO I positively modulated the action of ciprofloxacin, cefepime, and ceftriaxone. After the first hour of treatment with MICLaEO I, the cell viability of the strains showed a 5 log10 CFU/mL reduction, and the LaEO I-CIP association was able to inhibit growth during the first 6 h of the test. Regarding the anti-biofilm activity, MICLaEO I was able to reduce the biofilm mass of Salmonella typhi by 61.2% and of Shigella dysenteriae by 38.9%. MICLaEO I was not able to eradicate the preformed biofilm; however, there was a reduction in the biofilm microbial viability. LaEO I has the potential to be used as an antimicrobial agent and interferes with biofilm formation; also, it is able to reduce cell viability in preformed biofilm and synergistically modulate the activity of ciprofloxacin.

Pneumonia with pleural empyema caused by Salmonella Typhi in an immunocompetent child living in a non-endemic country

Extra-intestinal complications of Salmonella Typhi (S. Typhi) infections usually occur in endemic countries and in patients with underlying risk conditions. A 14-year-old immunocompetent girl was admitted with respiratory distress owing to S. Typhi pneumonia and pleural empyema. She was a native of Ivory Coast but had lived in France for 4 years and had not travelled abroad for several years. There were no gastro-intestinal symptoms and no S. Typhi carriage was detected in her family. She recovered completely with ceftriaxone and ciprofloxacin and pleural drainage was not required. An atypical presentation of S. Typhi should be considered even in settings where there are no risk factors.

Quinolone susceptibility and genetic characterization of Salmonella enterica subsp. enterica isolated from pet turtles

Turtle-borne Salmonella enterica owns significance as a leading cause in human salmonellosis. The current study aimed to determine the quinolone susceptibility and the genetic characteristics of 21 strains of S. enterica subsp. enterica isolated from pet turtles. Susceptibility of four antimicrobials including nalidixic acid, ciprofloxacin, ofloxacin, and levofloxacin was examined in disk diffusion and MIC tests where the majority of the isolates were susceptible to all tested quinolones. In genetic characterization, none of the isolates were positive for qnr or aac(6')-Ib genes and no any target site mutations could be detected in gyrA, gyrB, and parC quinolone resistance determining regions (QRDR). In addition, neighbor-joining phylogenetic tree derived using gyrA gene sequences exhibited two distinct clads comprising; first, current study isolates, and second, quinolone-resistant isolates of human and animal origin. All results suggest that studied strains of S. enterica subsp. enterica isolated from pet turtles are susceptible to quinolones and genetically more conserved with regards to gyrA gene region.

Strong influence of livestock environments on the emergence and dissemination of distinct multidrug-resistant phenotypes among the population of non-typhoidal Salmonella

The problem of emergence and dissemination of multidrug resistance, especially among Gram-negative bacteria, has reached alarming levels. This increases the need to develop surveillance methods that more effectively and accurately provide information about the emergence and spread of multidrug-resistant organisms. In this study, using a well-defined population of non-typhoidal Salmonella (NTS) isolates associated with avian, bovine and porcine hosts, we found that the livestock environments had a specific (P < 0.005) and profound (P < 0.005) effect on the evolution of multidrug-resistant phenotypes among population of NTS isolates. The MDR pattern containing penicillins, tetracyclines and macrolides and the evolving counterparts (i.e., penicillins, tetracyclines and macrolides + other antibiotic classes) were significantly (P < 0.005) associated with NTS isolates of porcine origin. Similarly, MDR patterns containing folate pathway inhibitors, macrolides and aminocyclitol or containing penicillins, cephalosporins, tetracyclines, phenicols and macrolides were significantly associated with avian (P < 0.005) and bovine (P < 0.005) NTS isolates, respectively. Furthermore, STRUCTURE, an evolutionary analysis, clearly showed that the host origin (i.e., livestock environment), and not the genetic background of different NTS serovars, was the most determinative factor for acquisition and spread of MDR phenotypes. In addition, we described a novel non-synonymous mutation, located outside of the QRDR at position 864 of GyrA, that was likely associated with fluoroquinolone resistance.

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.

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

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

Clinical trial registration: ISRCTN63006567.

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

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

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

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

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

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

SOS response and its regulation on the fluoroquinolone resistance

Bacteria can survive fluoroquinolone antibiotics (FQs) treatment by becoming resistant through a genetic change-mutation or gene acquisition. The SOS response is widespread among bacteria and exhibits considerable variation in its composition and regulation, which is repressed by LexA protein and derepressed by RecA protein. Here, we take a comprehensive review of the SOS gene network and its regulation on the fluoroquinolone resistance. As a unique survival mechanism, SOS may be an important factor influencing the outcome of antibiotic therapy in vivo.