[Resistance to quinolones and beta-lactams in Salmonella enterica due to mutations in topoisomerase-encoding genes, altered cell permeability and expression of an active efflux system]

Assessment of multidrug-resistant profile, multi-locus sequence typing and efflux pump activity in Salmonella Typhimurium isolated from hospital sewage

Salmonella enterica serovar Typhimurium is becoming a leading cause of gastroenteritis and mortality. The use of antibiotics has increased natural resistance of S. Typhimurium to antibiotics. This study aims to isolate and characterize multi-drug-resistant (MDR) Salmonella strains from hospital sewage samples in Bhopal City, central India. The MDR isolates were characterized by molecular identification, antimicrobial resistance patterns, multi-locus sequence typing, and efflux pump activity. Specific genes (hilA, stn, invA, typh, and iroB) were used to confirm S. Typhimurium isolates. The Kirbey-Bauer method was employed to profile antimicrobial resistance using 20 antibiotics. Multi-locus sequence typing confirmed S. Typhimurium using seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thr). Out of five strains, only four were confirmed as S. Typhimurium during MLST analysis. Efflux pump activity was determined using the ethidium bromide (EtBr) cartwheel test. Of the 160 isolates, 38 were presumptively confirmed as S. Typhimurium based on biochemical characterization, and only five MDR Salmonella strains were selected for their resistance against most antibiotics. Efflux pump activity revealed that five out of the four MDR isolates did not retain EtBr inside the cells, indicating pronounced efflux activity. Additionally, the isolated strains showed a specific correlation between the antimicrobial phenotypes and genotypes. The results of this study provide a better understanding of the characterization of S. Typhimurium serotype in Bhopal City. Future studies should focus on understanding changing antimicrobial resistance patterns, pathogenicity, and the genetic background of Salmonella serotypes. Further surveillance activities for antimicrobial-resistant Salmonella in different environmental sources should be prioritized.

Molecular Detection of Integrons, Colistin and β-lactamase Resistant Genes in Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Chickens and Rats Inhabiting Poultry Farms

The rapid growth of multidrug-resistant Salmonella is a global public health concern. The aim of this study was to detect integrons, colistin and β-lactamase resistance genes in Salmonella enteritidis and typhimurium. A total of 63 isolates of S. enteritidis (n = 18) and S. typhimurium (n = 45) from fecal samples of layers and rats at chicken farms were screened for antibiotic resistant genes. Conventional PCR was performed for the detection of integrons (classes 1, 2, and 3), colistin (mcr-1-5) and β-lactamase (bla_CTX-M, bla_CTX-M-1, bla_CTX-M-2, bla_CTX-M-9, bla_CTX-M-15, bla_TEM, bla_SHV, and bla_OXA) resistant genes. Of these isolates, 77% and 27% of S. typhimurium and S. enteritidis harboured the mcr-4 encoded gene for colistin, respectively. The prevalence of class 1 integrons for S. typhimurium and S. enteritidis was 100% for each serovar, while for class 2 integrons of S. typhimurium and S. enteritidis it was 49% and 33% respectively, while class 3 integron genes was not detected. Our study also detected high levels of β-lactamase encoding genes (bla gene), namely bla_CTX-M, bla_CTX-M-1, bla_CTX-M-9 and bla_TEM from both S. typhimurium and S. enteritidis. This, to our knowledge, is the first report of mcr-4 resistance gene detection in Salmonella serovars in South Africa. This study also highlights the importance of controlling rats at poultry farms in order to reduce the risk of transmission of antibiotic resistance to chickens and eventually to humans.

Development of phage-based assay to differentiate ciprofloxacin resistant and sensitive Salmonella Typhimurium

This study was designed to evaluate the possibility of using phage-amplification assay for discriminating between antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium. The characteristics of Salmonella phage PBST32 were determined by adsorption rate, one-step growth curve, and lytic activity. The ability of phage-based method to detect S. Typhimurium ATCC 19585 (ST^CIP) was determined in single culture and bacterial mixtures of S. Typhimurium ATCC 19585 (ST^WT), Klebsiella pneumoniae, and Staphylococcus aureus. The adsorption rates of PBST32 were 95% and 93% against ST^WT and ST^CIP after 20 min, respectively. The PBST32 showed latent period of 20 min and average burst size of 90 against ST^WT and ST^CIP. The ST^CIP was selectively detected in mixtures of S. aureus, K. pneumoniae, and ST^WT by phage amplification assay. These results provide useful information for designing phage amplification method that can differentially detect antibiotic-resistant pathogens.

Antiquorum sensing and antibiofilm potential of biosynthesized silver nanoparticles of Myristica fragrans seed extract against MDR Salmonella enterica serovar Typhi isolates from asymptomatic typhoid carriers and typhoid patients

Globally, Salmonella infection poses a major public health problem. Here, we report antibiofilm activity and quorum sensing inhibition of aqueous seeds extract of Myristica fragrans (nutmeg) and biosynthesized silver nanoparticles (AgNPs) against multidrug resistant (MDR) Salmonella enterica serovar Typhi (S. Typhi) isolated from typhoid patients and asymptomatic carriers. S. Typhi isolates revealed higher percentage (46%) of biofilm production identified by tissue culture plate (TCP) than Congo red agar (CRA) and tube adherence (TA) methods. The inhibition of biofilm-producing MDR S. Typhi isolates and pigment production of Chromobacterium violaceum (indicator bacteria) demonstrated the quorum sensing potential of nutmeg. The aqueous seed extract of nutmeg exhibited 87% of antibiofilm activity, while the biosynthesized AgNPs showed 99.1% of antibiofilm activity. Molecular docking studies of bioactive compounds of nutmeg against transcriptional regulatory protein RcsB and sensor kinase protein RcsC revealed interaction with the target proteins. It is proposed that biosynthesized AgNPs could be used as one of the effective candidates in treating asymptomatic typhoid carriers or typhoid patients and to control the subsistence of biofilm-producing S. Typhi strains or other pathogenic bacteria in the environment or industrial settings.

Combined effect of bacteriophage and antibiotic on the inhibition of the development of antibiotic resistance in Salmonella typhimurium

This study was designed to evaluate the combined effects of bacteriophage and antibiotic on the reduction of the development of antibiotic-resistance in Salmonella typhimurium LT2. The susceptibilities of S. typhimurium to ciprofloxacin and erythromycin were increased when treated with bacteriophages, showing more than 10% increase in clear zone sizes and greater than twofold decrease in minimum inhibitory concentration values. The growth of S. typhimurium was effectively inhibited by the combination of bacteriophage P22 and ciprofloxacin. The combination treatment effectively reduced the development of antibiotic resistance in S. typhimurium. The relative expression levels of efflux pump-related genes (acrA, acrB, and tolC) and outer membrane-related genes (ompC, ompD, and ompF) were decreased at all treatments. This study provides useful information for designing new antibiotic therapy to control antibiotic-resistant bacteria.

Salicylic Acid Reduces OmpF Expression, Rendering Salmonella enterica Serovar Typhimurium More Resistant to Cephalosporin Antibiotics

Salmonella enterica serovar Typhimurium is one of the most important bacterial pathogens causing diarrhea. The resistance of S. typhimurium to antimicrobial agents, which has recently been isolated from patients, is causing serious problems. We investigated the effects of salicylic acid (Sal) and acetyl salicylate (AcSal) on the susceptibility of S. typhimurium to cephalosporin antibiotics, which are known to increase resistance to cephalosporin and quinolone antibiotics. The MIC of cephalosporin antibiotics was higher than that of the media without Sal. The rate of accumulation of ethidium bromide (EtBr) in the bacteria by the outer membrane protein (Omp) was not different from that of the bacteria cultured in the medium containing Sal. However, Carbonyl cyanide-m-chlorophenylhydrazone (CCCP), an inhibitor of bacterial efflux pumps, significantly reduced the rate of accumulation of EtBr in bacteria cultured on Sal containing medium. In the medium containing CCCP, the MIC of the antimicrobial agent tended to decrease as compared with the control. In addition, the MIC of the bacteria treated with CCCP and Sal was higher than that of the antimicrobial agent against the CCCP treated experimental bacteria. These results suggest that Sal decreases the expression of OmpF in the Omp of S. typhimurium and reduces the permeability of cephalosporin antibiotics to bacteria, which may induce tolerance to cephalosporin antibiotics.

Characterization of β-lactamase- and efflux pump-mediated multiple antibiotic resistance in Salmonella Typhimurium

This study aimed to assess the β-lactamase- and efflux pump-mediated antibiotic resistance in Salmonella Typhimurium (WT-ST), ciprofloxacin-induced antibiotic-resistant S. Typhimurium (CI-ST), and clinically-acquired antibiotic-resistant S. Typhimurium (CA-ST). The β-lactamase activities were significantly increased up to 63 μmol/min/mL in CA-ST and 24 μmol/min/mL in CI-ST when compared to WT-ST (13 μmol/min/mL). The highest efflux pump activity was observed in CI-ST and CA-ST, showing more than 45%. The antibiotic susceptibilities of WT-ST, CI-ST, and CA-ST were increased in the presence of β-lactamase and efflux pump inhibitors. CA-ST showed the highest activity in AcrD, MdtABC, EmrAB, MdtK, and MacAB efflux pumps. The repressed ompF were responsible for the decreased susceptibility of CA-ST to ampicillin (MIC > 512 μg/mL). This study would provide useful information for better understating of the development of multidrug resistance in association with β-lactamase and efflux pump activities and designing new antibiotic chemotherapy in combination with inhibitors.

Emergence of Ciprofloxacin-Resistant Salmonella enterica Serovar Typhi in Italy

In developed countries, typhoid fever is often associated with persons who travel to endemic areas or immigrate from them. Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi. Because of the emergence of antimicrobial resistance to standard first-line drugs, fluoroquinolones are the drugs of choice. Resistance to ciprofloxacin by this Salmonella serovar represents an emerging public health issue. Two S. enterica ser. Typhi strains resistant to ciprofloxacin (CIP) were reported to the Italian surveillance system for foodborne and waterborne diseases (EnterNet-Italia) in 2013. The strains were isolated from two Italian tourists upon their arrival from India. A retrospective analysis of 17 other S. enterica ser. Typhi strains isolated in Italy during 2011–2013 was performed to determine their resistance to CIP. For this purpose, we assayed for susceptibility to antimicrobial agents and conducted PCR and nucleotide sequence analyses. Moreover, all strains were typed using pulsed-field gel electrophoresis to evaluate possible clonal relationships. Sixty-eight percent of the S. enterica ser. Typhi strains were resistant to CIP (MICs, 0.125–16 mg/L), and all isolates were negative for determinants of plasmid-mediated quinolone resistance. Analysis of sequences encoding DNA gyrase and topoisomerase IV subunits revealed mutations in gyrA, gyrB, and parC. Thirteen different clonal groups were detected, and the two CIP-resistant strains isolated from the individuals who visited India exhibited the same PFGE pattern. Because of these findings, the emergence of CIP-resistant S. enterica ser. Typhi isolates in Italy deserves attention, and monitoring antibiotic susceptibility is important for efficiently managing cases of typhoid fever.

Contribution of different mechanisms to the resistance to fluoroquinolones in clinical isolates of Salmonella enterica

Objectives

To study the potential factors include gene mutation, efflux pump and alteration of permeability associated with quinolone-resistance of Salmonella enterica strains isolated from patients with acute gastroenteritis and to evaluate the degree of synergistic activity of efflux pump inhibitors when combined with ciprofloxacin against resistant isolates.

Methods

Antimicrobial resistance patterns of fifty-eight Salmonella isolates were tested. Five isolates were selected to study the mechanism of resistance associated with quinolone group, including mutation in topoisomerase-encoding gene, altered cell permeability, and expression of an active efflux system. In addition, the combination between antibiotics and efflux pump inhibitors to overcome the microbial resistance was evaluated.

Results

Five Salmonella isolates totally resistant to all quinolones were studied. All isolates showed alterations in outer membrane proteins including disappearance of some or all of these proteins (Omp-A, Omp-C, Omp-D and Omp-F). Minimum inhibitory concentration values of ciprofloxacin were determined in the presence/absence of the efflux pump inhibitors: carbonyl cyanide m-chlorophenylhydrazone, norepinephrin and trimethoprim. Minimum inhibitory concentration values for two of the isolates were 2–4 fold lower with the addition of efflux pump inhibitors. All five Salmonella isolates were amplified for gyrA and parC genes and only two isolates were sequenced. S. Enteritidis 22 had double mutations at codon 83 and 87 in addition to three mutations at parC at codons 67, 76 and 80 whereas S. Typhimurium 57 had three mutations at codons 83, 87 and 119, but no mutations at parC.

Conclusions

Efflux pump inhibitors may inhibit the major AcrAB-TolC in Salmonella efflux systems which are the major efflux pumps responsible for multidrug resistance in Gram-negative clinical isolates.

Bacteraemia with pleural effusions complicating typhoid fever caused by high-level ciprofloxacin-resistant Salmonella enterica serotype Typhi

An unusual case of bacteraemia with bilateral pleural effusion caused by Salmonella enterica serotype Typhi in a 10-year-old previously healthy girl is reported. The organism was isolated from pleural fluid aspirate and from blood, and exhibited high-level ciprofloxacin resistance (MIC 16 μg/ml) associated with triple mutations in the QRDRs of the gyrA and parC genes leading to the amino-acid changes Ser83→Phe and Asp87→Asn in gyrA and Ser80→Ile in parC. The patient was successfully treated with parenteral ceftriaxone and intercostal chest tube drainage. The case is notable because of the important issue of antimicrobial resistance in S. Typhi and the therapeutic dilemma faced by clinicians regarding the empirical use of ciprofloxacin and newer fluoroquinolones.

Risk factors for antimicrobial resistance among the Escherichia coli strains isolated from Korean patients with acute uncomplicated cystitis: a prospective and nationwide study

We investigated the risk factors for resistance to ciprofloxacin, cefazolin, ampicillin and co-trimoxazole in Escherichia coli isolates from urine of Korean female patients with acute uncomplicated cystitis (AUC). A total of 225 patients and their E. coli isolates were prospectively and nationwidely enrolled between May and October, 2006. All the antimicrobials did not show any differences according to the age group. A higher rate of ciprofloxacin resistance was observed in the south (OR: 3.04, 95% CI: 1.19-7.80 for Chungcheong-do & Jeolla-do; OR: 3.04, 95% CI: 1.22-7.58 for Gyeongsang-do) compared to Gyeonggi-do. Two recurrences of AUC in the past year was an important risk factor for antimicrobial resistance (ciprofloxacin; OR: 6.71, 95% CI: 1.86-24.11 and cefazolin; OR: 5.72, 95% CI: 1.20-27.25). However, the resistance to co-trimoxazole and ampicillin was not associated with any of the risk factors. This study also revealed the pattern of multi-drugs resistance in ciprofloxacin resistant E. coli strains. In conclusion, for Korean patients with two more recurrences of AUC in the past year, it is strongly recommended to perform an antimicrobial sensitivity test with a urine sample before empirical treatment.

Fitness costs and stability of a high-level ciprofloxacin resistance phenotype in Salmonella enterica serotype enteritidis: reduced infectivity associated with decreased expression of Salmonella pathogenicity island 1 genes

The fitness costs associated with high-level fluoroquinolone resistance were examined for phenotypically and genotypically characterized ciprofloxacin-resistant Salmonella enterica serotype Enteritidis mutants (104-cip and 5408-cip; MIC, >32 microg/ml). The stability of the fluoroquinolone resistance phenotype in both mutants was investigated to assess whether clones with better fitness could emerge in the absence of antibiotic selective pressure. Mutants 104-cip and 5408-cip displayed altered morphology on agar and by electron microscopy, reduced growth rates, motility and invasiveness in Caco-2 cells, and increased sensitivity to environmental stresses. Microarray data revealed decreased expression of virulence and motility genes in both mutants. Two clones, 104-revert and 1A-revertC2, with ciprofloxacin MICs of 3 and 2 microg/ml, respectively, were recovered from separate lineages of 104-cip after 20 and 70 passages, respectively, on antibiotic-free agar. All fitness costs, except motility, were reversed in 104-revert. Potential mechanisms associated with reversal of the resistance phenotype were examined. Compared to 104-cip, both 104-revert and 1A-revertC2 showed decreased expression of acrB and soxS but still overexpressed marA. Both acquired additional mutations in SoxR and ParC, and 1A-revertC2 acquired two mutations in MarA. The altered porin and lipopolysaccharide (LPS) profiles observed in 104-cip were reversed. In contrast, 5408-cip showed no reversal in fitness costs and maintained its high-level ciprofloxacin resistance for 200 passages on antibiotic-free agar. In conclusion, high-level ciprofloxacin resistance in S. Enteritidis is associated with fitness costs. In the absence of antibiotic selection pressure, isolates may acquire mutations enabling reversion to an intermediate-level ciprofloxacin resistance phenotype associated with less significant fitness costs.

Multiple regulatory pathways associated with high-level ciprofloxacin and multidrug resistance in Salmonella enterica serovar enteritidis: involvement of RamA and other global regulators

Mechanisms of antibiotic resistance were examined in nalidixic acid-resistant Salmonella enterica serovar Enteritidis field isolates displaying decreased susceptibility to ciprofloxacin and in in vitro-derived ciprofloxacin-resistant mutants (104-cip and 5408-cip). All field isolates harbored a single gyrA mutation (D87Y). Deletion of acrB and complementation with wild-type gyrA increased quinolone susceptibility. Selection for ciprofloxacin resistance was associated with the development of an additional gyrA (S83F) mutation in 104-cip, novel gyrB (E466D) and parE (V461G) mutations in 5408-cip, overexpression of acrB and decreased susceptibility to nonquinolone antibiotics in both mutants, and decreased OmpF production and altered lipopolysaccharide in 104-cip. Complementation of mutated gyrA and gyrB with wild-type alleles restored susceptibility to quinolones in 104-cip and significantly decreased the ciprofloxacin MIC in 5408-cip. Complementation of parE had no effect on quinolone MICs. Deletion of acrB restored susceptibility to ciprofloxacin and other antibiotics tested. Both soxS and marA were overexpressed in 104-cip, and ramA was overexpressed in 5408-cip. Inactivation of each of these global regulators lowered ciprofloxacin MICs, decreased expression of acrB, and restored susceptibility to other antibiotics. Mutations were found in soxR (R20H) and in soxS (E52K) in 104-cip and in ramR (G25A) in 5408-cip. In conclusion, both efflux activity and a single gyrA mutation contribute to nalidixic acid resistance and reduced ciprofloxacin sensitivity. Ciprofloxacin resistance and decreased susceptibility to multiple antibiotics can result from different genetic events leading to development of target gene mutations, increased efflux activity resulting from differential expression of global regulators associated with mutations in their regulatory genes, and possible altered membrane permeability.