Plasmid-mediated quinolone resistance in Salmonella enterica, United Kingdom

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.

Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidal Salmonella enterica Strains Isolated From Cambodian Informal Markets

Non-typhoidal Salmonella enterica is a pathogen of global importance, particularly in low and middle-income countries (LMICs). The presence of antimicrobial resistant (AMR) strains in market environments poses a serious health threat to consumers. In this study we identified and characterized the genotypic and phenotypic AMR profiles of 81 environmental S. enterica strains isolated from samples from informal markets in Cambodia in 2018–2019. AMR genotypes were retrieved from the NCBI Pathogen Detection website (https://www.ncbi.nlm.nih.gov/pathogens/) and using ResFinder (https://cge.cbs.dtu.dk/services/) Salmonella pathogenicity islands (SPIs) were identified with SPIFinder (https://cge.cbs.dtu.dk/services/). Susceptibility testing was performed by broth microdilution according to the Clinical and Laboratory Standards Institute (CLSI) standard guidelines M100-S22 using the National Antimicrobial Resistance Monitoring System (NARMS) Sensititre Gram Negative plate. A total of 17 unique AMR genes were detected in 53% (43/81) of the isolates, including those encoding tetracycline, beta-lactam, sulfonamide, quinolone, aminoglycoside, phenicol, and trimethoprim resistance. A total of 10 SPIs (SPI-1, 3–5, 8, 9, 12–14, and centisome 63 [C63PI]) were detected in 59 isolates. C63PI, an iron transport system in SPI-1, was observed in 56% of the isolates (n = 46). SPI-1, SPI-4, and SPI-9 were present in 13, 2, and 5% of the isolates, respectively. The most common phenotypic resistances were observed to tetracycline (47%; n = 38), ampicillin (37%; n = 30), streptomycin (20%; n = 16), chloramphenicol (17%; n = 14), and trimethoprim-sulfamethoxazole (16%; n = 13). This study contributes to understanding the AMR genes present in S. enterica isolates from informal markets in Cambodia, as well as support domestic epidemiological investigations of multidrug resistance (MDR) profiles.

Plasmid-mediated quinolone resistance genes transfer among enteric bacteria isolated from human and animal sources

This research investigates the transferability of plasmid-mediated quinolone resistance (PMQR) genes among enteric bacteria isolates in human and animal samples, as well as its implication on resistance of recipient cells. A total of 1,964 strains of five different enteric bacteria species (Escherichia coli, Salmonella sp., Shigella sp., Klebsiella sp. and Aeromonas sp.) were screened for plasmid-mediated quinolone resistance (PMQR) genes from a population of quinolone resistant (Q-r) isolates. Screening for PMQR isolates was achieved by plasmid curing using sub-lethal concentration of Sodium Dodecyl Sulphate and PMQR genes (qnrA, qnrB, qnrS, Aac(6')-Ib-crand Qep A) were detected by polymerase chain reaction (PCR). Conjugation and transformation experiments were attempted to ascertain transfer of genes from the Q-r isolates to a susceptible, standard recipient, E. coli J53-2. The minimum inhibitory concentration (MIC) was determined before and after gene transfer, using E-test strips. Results indicate that percentage resistance to the quinolones (Qs): Nalidixic acid, Ciprofloxacin, Pefloxacin and Ofloxacin determined by agar plate diffusion technique stood at 52.6, 47.3, 50.5, 70.6 and 46.0% for Escherichia coli, Salmonella sp., Shigellasp., Klebsiella sp. and Aeromonas sp. respectively. Analysis of variance indicated the occurrence of significant differences (F, 46.77-613.30; 0.00) in the resistance to each tested Qs. Generally, Human isolates showed greater resistance than Animal isolates (57.4 vs 47.2%). Investigation with specific primers indicated 11, 15, 7, 1 and 0 for qnrA, qnrB, qnrS, qepA and Aac(6')-Ib-cr genes respectively, out of 1018 Q-r and 29 PMQR isolates. Gene transfer experiments indicated the transfer of all genes except qepA either by conjugation or transformation. The MIC of tested Qs on recipient bacterium before gene transfer greatly increased from 0.0625 to 0.25 µg/mL, after transfer. This study demonstrates that PMQR genes amongst enteric bacteria in the Niger delta of Nigeria were transferable and transfer conferred a higher Q- resistance on recipient bacterium.

Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in Nigeria

Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.

Actinobacillus pleuropneumoniae Eradication with Enrofloxacin May Lead to Dissemination and Long-Term Persistence of Quinolone Resistant Escherichia coli in Pig Herds

Norway has a favourable situation with regard to health status and antimicrobial usage in the pig production sector. However, one of the major disease-causing agents in the commercial pig population is Actinobacillus pleuropneumoniae (APP). In some herds, APP eradication has been performed by using enrofloxacin in combination with a partial herd depopulation. The aim of this study was to investigate the long-term effects of a single treatment event with enrofloxacin on the occurrence of quinolone resistant Escherichia coli (QREC). The study was designed as a retrospective case/control study, where the herds were selected based on treatment history. Faecal samples were taken from sows, gilts, fattening pigs and weaners for all herds where available. A semi-quantitative culturing method was used to identify the relative quantity of QREC in the faecal samples. A significant difference in overall occurrence and relative quantity of QREC was identified between the case and control herds, as well as between each animal age group within the case/control groups. The results indicate that a single treatment event with enrofloxacin significantly increased the occurrence of QREC in the herd, even years after treatment and with no subsequent exposure to quinolones.

Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies

We sequenced 25 isolates of phenotypically multidrug-resistant Salmonella Indiana (n = 11), Typhimurium (n = 8), and Enteritidis (n = 6) using both MinION long-read [SQK-LSK109 and flow cell (R9.4.1)] and MiSeq short-read (Nextera XT and MiSeq Reagent Kit v2) sequencing technologies to determine the advantages of each approach in terms of the characteristics of genome structure, antimicrobial resistance (AMR), virulence potential, whole-genome phylogeny, and pan-genome. The MinION reads were base-called in real-time using MinKnow 3.4.8 integrated with Guppy 3.0.7. The long-read-only assembly, Illumina-only assembly, and hybrid assembly pipelines of Unicycler 0.4.8 were used to generate the MinION, MiSeq, and hybrid assemblies, respectively. The MinION assemblies were highly contiguous compared to the MiSeq assemblies but lacked accuracy, a deficiency that was mitigated by adding the MiSeq short reads through the Unicycler hybrid assembly which corrected erroneous single nucleotide polymorphisms (SNPs). The MinION assemblies provided similar predictions of AMR and virulence potential compared to the MiSeq and hybrid assemblies, although they produced more total false negatives of AMR genotypes, primarily due to failure in identifying tetracycline resistance genes in 11 of the 19 MinION assemblies of tetracycline-resistant isolates. The MinION assemblies displayed a large genetic distance from their corresponding MiSeq and hybrid assemblies on the whole-genome phylogenetic tree, indicating that the lower read accuracy of MinION sequencing caused incorrect clustering. The pan-genome of the MinION assemblies contained significantly more accessory genes and less core genes compared to the MiSeq and hybrid assemblies, suggesting that although these assemblies were more contiguous, their sequencing errors reduced accurate genome annotations. Our research demonstrates that MinION sequencing by itself provides an efficient assessment of the genome structure, antimicrobial resistance, and virulence potential of Salmonella; however, it is not sufficient for whole-genome phylogenetic and pan-genome analyses. MinION in combination with MiSeq facilitated the most accurate genomic analyses.

Prevalence of Salmonella Isolates and Their Distribution Based on Whole-Genome Sequence in a Chicken Slaughterhouse in Jiangsu, China

Salmonella has been known as the most important foodborne pathogen, which can infect humans via consuming contaminated food. Chicken meat has been known as an important vehicle to transmit Salmonella by the food supply chain. This study determined the prevalence, antimicrobial resistance, and genetic characteristics of Salmonella at different chicken slaughtering stages in East China. In total, 114 out of 200 (57%) samples were Salmonella positive, while Salmonella contamination was gradually increasing from the scalding and unhairing stage (17.5%) to the subdividing stage (70%) throughout the slaughtering. Whole-genome sequencing (WGS) was then performed to analyze the serotype, antimicrobial resistance gene profiles, and genetic relationship of all Salmonella isolates. The most common serotypes were S. Kentucky (51/114, 44.7%) and S. Enteritidis (37/114, 32.5%), which were distributed throughout the four slaughtering stages, and were also identified in the corresponding environments. The multilocus sequence typing (MLST) analysis revealed that seven sequence types (STs) were occupied by six different serotypes, respectively. Only S. Kentucky had two STs, ST314 was the predominant ST shared by 50 isolates, while the ST198 has 1 isolate. The antimicrobial resistance gene analysis demonstrated that most of the strains belonging to S. Kentucky (39/51, 76.5%) and S. Indiana (15, 100%) contained over five groups of antimicrobial resistance genes. Based on the core genome analysis, 50 S. Kentucky isolates were genetically identical, indicating that one S. Kentucky strain with the same genetic background was prevalent in the chicken slaughtering line. Although 37 S. Enteritidis isolates only had three different antimicrobial resistance gene profiles, the core genome sequence analysis subtyped these S. Enteritidis isolates into five different clusters, which revealed the diverse genetic background of S. Enteritidis in the slaughterhouse. The antimicrobial resistance phenotypes were consistent with the presence of the corresponding resistance genes of S. Kentucky and S. Enteritidis, including tetA, floR, blaTEM-1B, strA/B, sul1/sul2, and gyrA (D87Y). Our study observed a high prevalence of Salmonella in the chicken slaughter line and identified the slaughtering environment as a main source of causing Salmonella cross-contamination during chicken slaughtering. Further studies will be needed to limit the transmission of Salmonella in the slaughterhouse.

Chromosomal and plasmid-mediated fluoroquinolone resistance in human Salmonella enterica infection in Ghana

Background

Salmonella infection poses significant public health threat globally, especially in resource-limited countries. Emergence and spread of antibiotic resistant strains to fluoroquinolones have led to treatment failures and increased mortality in Salmonella infection. However, there is dearth of information regarding mechanisms of resistance to fluoroquinolones in Ghana. This study therefore sought to identify chromosomal mutations and plasmid-mediated resistance as possible mechanisms of fluoroquinolone resistance from clinical isolates in Ghana.

Methods

This was a retrospective study of archived isolates biobanked at Kumasi Centre for Collaborative Research in Tropical Medicine, Ghana. Isolates were obtained from blood, stool and oropharynx samples at two hospitals, between May, 2016 and January, 2018. Salmonella identification was done using standard microbiological protocols and antibiotic susceptibility testing performed by Kirby-Bauer disc diffusion method. Isolates with intermediate susceptibility and/or resistance to nalidixic acid and/or ciprofloxacin were selected and examined for chromosomal mutations by Sanger sequencing and plasmid-mediated resistance by PCR.

Results

Of 133 biobanked isolates cultured, 68 (51.1%) and 16 (12%) were identified as Salmonella Typhi and non-typhoidal Salmonella (NTS), respectively. Sequence analysis of gyrA gene revealed the presence of 5 different nonsynonymous mutations, with the most frequent mutation (Ile203Ser) occurring in 12 out of 13 isolates tested. Gyrase B (gyrB) gene had 1 nonsynonymous mutation in 3 out of 13 isolates, substituting phenylalanine with leucine at codon 601 (Phe601Leu). No mutation was observed in parC and parE genes. Two NTS isolates were found to harbour qnrS plasmid-mediated resistant gene of molecular size 550 bp with high ciprofloxacin MIC of 0.5 μg/ml.

Conclusion

This study reports for the first time in Ghana plasmid-mediated fluoroquinolone resistant gene qnrS in Salmonella clinical isolates. Nonsynonymous mutations of gyrA and gyrB genes likely to confer Salmonella reduced susceptibility to ciprofloxacin were also reported.

Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets

Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.

Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing

Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis. A total of 39 resistance genes were identified, such as aminoglycoside, tetracycline, sulfonamide, trimethoprim, beta-lactam, fluoroquinolone, phenicol and macrolide, as well as the occurrence of point mutations in some of the genes such as gyrA, gyrB, parC and parE. A total of 65 (72.2%) out of 90 S. Typhimurium strains studied were phenotypically resistant to sulfonamides, 44 (48.9%) strains were streptomycin resistant, 27 (30%) strains were resistant to tetracycline, 21 (23.3%) strains were gentamicin resistant, and seven (7.8%) strains were resistant to ceftriaxone. In the gyrA gene, it was observed the following amino acid substitutions: Asp(87)→Gly, Asp(87)→Asn, Ser(83)→Phe, Ser(83)→Tyr. Phylogenetic results placed the 90 S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in foods. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforces their potential hazard for humans and the risk in foods in Brazil.

Plasmid-mediated quinolone resistance in human non-typhoidal Salmonella infections: An emerging public health problem in the United States

Invasive Salmonella infections in adults are commonly treated with fluoroquinolones, a critically important antimicrobial class. Historically, quinolone resistance was the result of chromosomal mutations, but plasmid-mediated quinolone resistance (PMQR) has emerged and is increasingly being reported in Enterobacteriaceae worldwide. PMQR may facilitate the spread of quinolone resistance, lead to higher-level quinolone resistance, and make infections harder to treat. To better understand the epidemiology of PMQR in non-typhoidal Salmonella causing human infections in the United States, we looked at trends in quinolone resistance among isolates submitted to the Centers for Disease Control and Prevention. We reviewed demographic, exposure and outcome information for patients with isolates having a PMQR-associated phenotype during 2008-2014 and tested isolates for quinolone resistance mechanisms. We found that PMQR is emerging among non-typhoidal Salmonella causing human infections in the United States and that international travel, reptile and amphibian exposure, and food are likely sources of human infection.

Typhoid fever: issues in laboratory detection, treatment options & concerns in management in developing countries

Multidrug-resistant Salmonella enterica subsp. enterica serovar Typhi (resistant to ampicillin, chloramphenicol and cotrimoxazole), was significantly reduced with the increased usage of fluoroquinolones and azithromycin. This has led to declining multidrug resistance rates in India with increasing ciprofloxacin nonsusceptibility rates and clinical failures due to azithromycin. However, for the available agents such as ceftriaxone, azithromycin and fluoroquinolones, the dose and duration for treatment is undefined. The ongoing clinical trials for typhoid management are expected to recommend the defined dose and duration for better clinical outcome. We made an attempt to summarize the issues in laboratory detection, treatment options and responses, and the concerns in clinical practice seen in the developing countries.

Typhoid fever is an important cause of mortality in developing countries and is a major public health concern. Cephalosporins or azithromycin are the drugs of choice for treating infection caused by the reduced fluoroquinolone susceptibility of S. Typhi. Emergence of cephalosporin resistance in S. Typhi and azithromycin-associated clinical and microbiological failure is of significant concern in developing countries. An approach of cephalosporin–azithromycin combination therapy has been suggested, which could be a potential alternative in treating uncomplicated S. Typhi infection in endemic areas. This review summarizes the field so far.

Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

Laboratory-based in vitro antimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidal Salmonella and correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred forty Salmonella of 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n = 59) in the 104 human isolates than in the 536 retail meat isolates (n = 36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum β-lactamases (ESBLs) (blaCTX-M1 and blaSHV2a) in retail meat isolates of Salmonella in the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidal Salmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.

High prevalence and molecular characteristics of multidrug-resistant Salmonella in pigs, pork and humans in Thailand and Laos provinces

This study aimed to examine occurrence and antimicrobial resistance characteristics of Salmonella from pigs, pork and humans in Thailand and Laos provinces. The samples were collected from pigs, carcasses and workers in slaughterhouses, retail pork and butchers in fresh markets and patients in hospitals in Thailand (n=729) and Laos (n=458). A total of 295 of 729 samples (34.6 %) collected in Thailand and 253 of 458 (47.4 %) samples collected in Laos were positive for Salmonella. A total of 548 Salmonella isolates from Thailand (n=295) and Laos (n=253) were further analysed. Serovar Typhimurium was the most common serotype in Thai (34 %) and Laos (20.6 %) samples. Approximately 2.4 % of Thai isolates produced extended-spectrum β-lactamase (ESBL). All the ESBL producers possessed blaCTX-M-14, some of which were horizontally transferred. Class 1 integrons were common in Thai (31.9 %) and Laos (39.1 %) isolates, but none were associated with SGI1. The resistance cassette dfrA12-aadA2 was the most common, while the least common was aadA2-linG (n=1). The dfrA12-aadA2 gene cassette in five isolates and aadA2-linG were located on conjugative plasmid. Three pork isolates were fluoroquinolone resistant and carried an amino acid substitute, Ser-83-Tyr, in GyrA. The qnrS gene was found in 7.1 and 5.5 % of the Thai and Laos isolates, respectively, while qnrB was carried in another Laos isolate (1.9 %). All ESBL producers carried qnrS. In conclusion, multidrug-resistant Salmonella was common in pigs, pork and human samples in this region. The bacteria carried mobile genetic elements and resistance genes on conjugative plasmids that could be readily transferred to other bacterial species.

Plasmid-mediated quinolone resistance

Three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998. Plasmid genes qnrA, qnrB, qnrC, qnrD, qnrS, and qnrVC code for proteins of the pentapeptide repeat family that protects DNA gyrase and topoisomerase IV from quinolone inhibition. The qnr genes appear to have been acquired from chromosomal genes in aquatic bacteria, are usually associated with mobilizing or transposable elements on plasmids, and are often incorporated into sul1-type integrons. The second plasmid-mediated mechanism involves acetylation of quinolones with an appropriate amino nitrogen target by a variant of the common aminoglycoside acetyltransferase AAC(6')-Ib. The third mechanism is enhanced efflux produced by plasmid genes for pumps QepAB and OqxAB. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. The plasmid-mediated mechanisms provide only low-level resistance that by itself does not exceed the clinical breakpoint for susceptibility but nonetheless facilitates selection of higher-level resistance and makes infection by pathogens containing PMQR harder to treat.

Mechanisms of drug resistance: quinolone resistance

Quinolone antimicrobials are synthetic and widely used in clinical medicine. Resistance emerged with clinical use and became common in some bacterial pathogens. Mechanisms of resistance include two categories of mutation and acquisition of resistance-conferring genes. Resistance mutations in one or both of the two drug target enzymes, DNA gyrase and DNA topoisomerase IV, are commonly in a localized domain of the GyrA and ParE subunits of the respective enzymes and reduce drug binding to the enzyme-DNA complex. Other resistance mutations occur in regulatory genes that control the expression of native efflux pumps localized in the bacterial membrane(s). These pumps have broad substrate profiles that include quinolones as well as other antimicrobials, disinfectants, and dyes. Mutations of both types can accumulate with selection pressure and produce highly resistant strains. Resistance genes acquired on plasmids can confer low-level resistance that promotes the selection of mutational high-level resistance. Plasmid-encoded resistance is due to Qnr proteins that protect the target enzymes from quinolone action, one mutant aminoglycoside-modifying enzyme that also modifies certain quinolones, and mobile efflux pumps. Plasmids with these mechanisms often encode additional antimicrobial resistances and can transfer multidrug resistance that includes quinolones. Thus, the bacterial quinolone resistance armamentarium is large.

How multidrug resistance in typhoid fever affects treatment options

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

Resistance to third-generation cephalosporins in human non-typhoidal Salmonella enterica isolates from England and Wales, 2010-12

OBJECTIVES

To identify the mechanism(s) underlying cefotaxime resistance in 118 of 21,641 (0.55%) non-typhoidal Salmonella enterica isolates collected from humans throughout England and Wales from January 2010 to September 2012.

METHODS

Non-duplicate isolates (n = 118) resistant to cefotaxime (MICs >1 mg/L) were screened by PCR for genes encoding CTX-M extended-spectrum β-lactamases (ESBLs) and associated ISEcp1-like elements, and for genes encoding acquired AmpC, SHV, TEM, VEB, PER and GES β-lactamases. Sequencing was used to identify specific alleles in selected isolates. Carbapenem resistance was sought by ertapenem disc screening.

RESULTS

Seventy-nine isolates (0.37% of all referred S. enterica) produced ESBLs, 37 isolates (0.17%) produced CMY-type AmpC enzymes, and 1 isolate had both enzyme types; the mechanism of cefotaxime resistance in 3 isolates could not be identified. Group 1 CTX-M genes were identified in 57 isolates belonging to 22 serotypes, with CTX-M-1 (n = 11), -15 (n = 9) and -55/57 (n = 8) the most prevalent alleles among the 29 (51%) investigated. CTX-M-2 (n = 5), -14 (n = 5), -8 (n = 1) and -65 (n = 1) were also identified. TEM-52 was identified in two isolates and SHV-12 in seven isolates. There was no evidence of carbapenem resistance. ESBL and AmpC genes were detected in both domestically acquired and travel-associated salmonellae. Eighty-nine isolates (75%) were multidrug resistant (resistant to at least three antimicrobial classes) and 42 (36%) had decreased susceptibility to ciprofloxacin (MICs 0.25-1 mg/L), with a further 13 (11%) isolates resistant (MICs >1 mg/L).

CONCLUSIONS

The prevalence of CTX-M and acquired AmpC genes in human non-typhoidal S. enterica from England and Wales is still low, but has increased from 0.03% in 2001-03 to 0.49% in 2010-12. Resistance to third-generation cephalosporins requires monitoring as it may reduce therapeutic options.

Occurrence of fluoroquinolones and fluoroquinolone-resistance genes in the aquatic environment

Fluoroquinolones (FQs) have been detected in aquatic environments in several countries. Long-term exposure to low levels of antimicrobial agents provides selective pressure, which might alter the sensitivity of bacteria to antimicrobial agents in the environment. Here, we examined FQ levels and the resistance of Escherichia coli (E. coli) to FQs by phenotyping and genotyping. In the aquatic environment in Osaka, Japan, ciprofloxacin, enoxacin, enfloxacin, lomefloxacin, norfloxacin, and ofloxacin were detected in concentrations ranging from 0.1 to 570 ng L(-1). FQ-resistant E. coli were also found. Although no obvious correlation was detected between the concentration of FQs and the presence of FQ-resistant E. coli, FQ-resistant E. coli were detected in samples along with FQs, particularly ciprofloxacin and ofloxacin. Most FQ-resistant E. coli carried mutations in gyrA, parC, and parE in quinolone resistance-determining regions. No mutations in gyrB were detected in any isolates. Amino acid changes in these isolates were quite similar to those in clinical isolates. Six strains carried the plasmid-mediated quinolone resistance determinant qnrS1 and expressed low susceptibility to ciprofloxacin and nalidixic acid: the minimum inhibitory concentrations ranged from 0.25 μg mL(-1) for ciprofloxacin, and from 8 to 16 μg mL(-1) for nalidixic acid. This finding confirmed that plasmids containing qnr genes themselves did not confer full resistance to quinolones. Because plasmids are responsible for much of the horizontal gene transfer, these genes may transfer and spread in the environment. To our knowledge, this is the first report of plasmid-mediated quinolone resistance determinant qnrS1 in the aquatic environment, and this investigation provides baseline data on antimicrobial resistance profiles in the Osaka area.

Inhibition of tissue inflammation and bacterial translocation as one of the protective mechanisms of Saccharomyces boulardii against Salmonella infection in mice

Growing evidences suggest that Saccharomyces boulardii (SB) is efficacious against bacterial infections and inflammatory bowel diseases. This study investigated the effects of treatment with SB provided in a murine model of typhoid fever. Mice were divided into two groups: (1) control animals challenged with Salmonella Typhimurium (ST), and (2) animals receiving SB, and then challenged with ST. At days 0, 1, 5, 10 and 15 post-challenge, animals were euthanized and tissues collected to analyze bacterial translocation, cytokines, signaling pathways and histological analysis. Survival rate and animal weight were also evaluated. Treatment with SB increased survival rate and inhibited translocation of bacteria after ST challenge. Histological data showed that SB also protected mice against liver damage induced by ST. SB decreased levels of inflammatory cytokines and activation of mitogen-activated protein kinases (p38, JNK and ERK1/2), phospho-IκB, p65-RelA, phospho-jun and c-fos in the colon, signal pathways involved in the activation of inflammation induced by ST. Further experiments revealed that probiotic effects were due, at least in part, to the binding of ST to the yeast. Such binding diminishes ST translocation, resulting in decreased activation of signaling pathways which lead to intestinal inflammation in a murine model of typhoid fever.

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.

Modification of Salmonella Typhimurium motility by the probiotic yeast strain Saccharomyces boulardii

Background

Motility is an important component of Salmonella enterica serovar Typhimurium (ST) pathogenesis allowing the bacteria to move into appropriate niches, across the mucus layer and invade the intestinal epithelium. In vitro, flagellum-associated motility is closely related to the invasive properties of ST. The probiotic yeast Saccharomyces boulardii BIOCODEX (S.b-B) is widely prescribed for the prophylaxis and treatment of diarrheal diseases caused by bacteria or antibiotics. In case of Salmonella infection, S.b-B has been shown to decrease ST invasion of T84 colon cell line. The present study was designed to investigate the impact of S.b-B on ST motility.

Methodology/Principal Findings

Experiments were performed on human colonic T84 cells infected by the Salmonella strain 1344 alone or in the presence of S.b-B. The motility of Salmonella was recorded by time-lapse video microscopy. Next, a manual tracking was performed to analyze bacteria dynamics (MTrackJ plugin, NIH image J software). This revealed that the speed of bacterial movement was modified in the presence of S.b-B. The median curvilinear velocity (CLV) of Salmonella incubated alone with T84 decreased from 43.3 µm/sec to 31.2 µm/sec in the presence of S.b-B. Measurement of track linearity (TL) showed similar trends: S.b-B decreased by 15% the number of bacteria with linear tract (LT) and increased by 22% the number of bacteria with rotator tract (RT). Correlation between ST motility and invasion was further established by studying a non-motile flagella-deficient ST strain. Indeed this strain that moved with a CLV of 0.5 µm/sec, presented a majority of RT and a significant decrease in invasion properties. Importantly, we show that S.b-B modified the motility of the pathogenic strain SL1344 and significantly decreased invasion of T84 cells by this strain.

Conclusions

This study reveals that S.b-B modifies Salmonella's motility and trajectory which may account for the modification of Salmonella's invasion.

In vitro activity of azithromycin against nontyphoidal Salmonella enterica

The in vitro activity of azithromycin against 1,237 nontyphoidal Salmonella enterica isolates collected from Finnish patients between 2003 and 2008 was investigated. Only 24 (1.9%) of the isolates tested and 15 (5.1%) of the 294 isolates with reduced fluoroquinolone susceptibility had azithromycin MICs of >or=32 microg/ml. These data show that azithromycin has good in vitro activity against nontyphoidal S. enterica, and thus, it may be a good candidate for clinical treatment studies of salmonellosis.

Plasmid-mediated quinolone resistance: a multifaceted threat

Although plasmid-mediated quinolone resistance (PMQR) was thought not to exist before its discovery in 1998, the past decade has seen an explosion of research characterizing this phenomenon. The best-described form of PMQR is determined by the qnr group of genes. These genes, likely originating in aquatic organisms, code for pentapeptide repeat proteins. These proteins reduce susceptibility to quinolones by protecting the complex of DNA and DNA gyrase or topoisomerase IV enzymes from the inhibitory effect of quinolones. Two additional PMQR mechanisms were recently described. aac(6')-Ib-cr encodes a variant aminoglycoside acetyltransferase with two amino acid alterations allowing it to inactivate ciprofloxacin through the acetylation of its piperazinyl substituent. oqxAB and qepA encode efflux pumps that extrude quinolones. All of these genes determine relatively small increases in the MICs of quinolones, but these changes are sufficient to facilitate the selection of mutants with higher levels of resistance. The contribution of these genes to the emergence of quinolone resistance is being actively investigated. Several factors suggest their importance in this process, including their increasing ubiquity, their association with other resistance elements, and their emergence simultaneous with the expansion of clinical quinolone resistance. Of concern, these genes are not yet being taken into account in resistance screening by clinical microbiology laboratories.

Interaction of Saccharomyces boulardii with Salmonella enterica serovar Typhimurium protects mice and modifies T84 cell response to the infection

Background

Salmonella pathogenesis engages host cells in two-way biochemical interactions: phagocytosis of bacteria by recruitment of cellular small GTP-binding proteins induced by the bacteria, and by triggering a pro-inflammatory response through activation of MAPKs and nuclear translocation of NF-κB. Worldwide interest in the use of functional foods containing probiotic bacteria for health promotion and disease prevention has increased significantly. Saccharomyces boulardii is a non-pathogenic yeast used as a probiotic in infectious diarrhea.

Methodology/Principal Findings

In this study, we reported that S. boulardii (Sb) protected mice from Salmonella enterica serovar Typhimurium (ST)-induced death and prevented bacterial translocation to the liver. At a molecular level, using T84 human colorectal cancer cells, we demonstrate that incubation with Sb before infection totally abolished Salmonella invasion. This correlates with a decrease of activation of Rac1. Sb preserved T84 barrier function and decreased ST-induced IL-8 synthesis. This anti-inflammatory effect was correlated with an inhibitory effect of Sb on ST-induced activation of the MAPKs ERK1/2, p38 and JNK as well as on activation of NF-κB. Electron and confocal microscopy experiments showed an adhesion of bacteria to yeast cells, which could represent one of the mechanisms by which Sb exerts its protective effects.

Conclusions

Sb shows modulating effects on permeability, inflammation, and signal transduction pathway in T84 cells infected by ST and an in vivo protective effect against ST infection. The present results also demonstrate that Sb modifies invasive properties of Salmonella.

Mechanisms of resistance in nontyphoidal Salmonella enterica strains exhibiting a nonclassical quinolone resistance phenotype

Nontyphoidal Salmonella enterica strains with a nonclassical quinolone resistance phenotype were isolated from patients returning from Thailand or Malaysia to Finland. A total of 10 isolates of seven serovars were studied in detail, all of which had reduced susceptibility (MIC > or = 0.125 microg/ml) to ciprofloxacin but were either susceptible or showed only low-level resistance (MIC < or = 32 microg/ml) to nalidixic acid. Phenotypic characterization included susceptibility testing by the agar dilution method and investigation of efflux activity. Genotypic characterization included the screening of mutations in the quinolone resistance-determining regions (QRDR) of gyrA, gyrB, parC, and parE by PCR and denaturing high-pressure liquid chromatography and the amplification of plasmid-mediated quinolone resistance (PMQR) genes qnrA, qnrB, qnrS, qnrD, aac(6')-Ib-cr, and qepA by PCR. PMQR was confirmed by plasmid analysis, Southern hybridization, and plasmid transfer. No mutations in the QRDRs of gyrA, gyrB, parC, or parE were detected with the exception of a Thr57-Ser substitution within ParC seen in all but the S. enterica serovar Typhimurium strains. The qnrA and qnrS genes were the only PMQR determinants detected. Plasmids carrying qnr alleles were transferable in vitro, and the resistance phenotype was reproducible in Escherichia coli DH5alpha transformants. These data demonstrate the emergence of a highly mobile qnr genotype that, in the absence of mutation within topoisomerase genes, confers the nontypical quinolone resistance phenotype in S. enterica isolates. The qnr resistance mechanism enables bacteria to survive elevated quinolone concentrations, and therefore, strains carrying qnr alleles may be able to expand during fluoroquinolone treatment. This is of concern since nonclassical quinolone resistance is plasmid mediated and therefore mobilizable.

Reduced fluoroquinolone susceptibility in Salmonella enterica isolates from travelers, Finland

We tested the fluoroquinolone susceptibility of 499 Salmonella enterica isolates collected from travelers returning to Finland during 2003–2007. Among isolates from travelers to Thailand and Malaysia, reduced fluoroquinolone susceptibility decreased from 65% to 22% (p = 0.002). All isolates showing nonclassical quinolone resistance were from travelers to these 2 countries.

Prevalence of plasmid-mediated quinolone resistance determinants in ESBL Enterobacteriaceae clinical isolates over a 1-year period in a French hospital

The prevalence of plasmid-mediated quinolone resistance (PMQR) determinants (qnrA, qnrB, qnrS, aac(6')-Ib-cr, and qepA) was investigated in a collection of 47 extended-spectrum β-lactamase (ESBL) producing enterobacterial isolates with reduced susceptibility to fluoroquinolones, recovered at Nantes University hospital, in 2006. qnr, aac(6')-Ib-cr, and qepA genes were screened by PCR, and positive results were subsequently confirmed by sequencing. The epidemiological relationship between positive isolates was studied by pulsed-field gel electrophoresis (PFGE). qnr-positive isolates were analyzed for antimicrobial susceptibility and presence of mutations in the quinolone resistance-determining region (QRDR) of gyrA and parC genes. ESBL genes were characterized by PCR and sequencing. Conjugation experiments were performed to determine whether the qnr-carrying plasmids were self-transferable. Two Klebsiella pneumoniae isolates (4.3%), not clonally related, harboured a qnrS1 gene, whereas no qnrA- or qnrB-positive isolate was detected. The aac(6')-Ib-cr gene was detected in 11 Escherichia coli and one K. pneumoniae isolates. None of the 47 isolates carried the qepA gene. ESBLs associated with QnrS1 were CTX-M-14 and CTX-M-15. The CTX-M-15 producing isolate was highly resistant to fluoroquinolones and harboured three mutations in the QRDR and two PMQR determinants (qnrS1 and aac(6')-Ib-cr). The CTX-M-14-producing isolate exhibited reduced susceptibility or resistance to fluoroquinolones without resistance to nalidixic acid. This strain harboured only a qnr gene on a single 170 kb transferable plasmid, without any mutation in the QRDR. In conclusion, our study showed that aac(6')-Ib-cr gene had occurred in multiclonal ESBL-producing enterobacterial isolates collected at Nantes University hospital in 2006, with a higher prevalence than qnr genes.

High prevalence of qnr genes in commensal enterobacteria from healthy children in Peru and Bolivia

A remarkable prevalence of qnrB (54%) and, at a lower level, of qnrS (14%) was discovered in pools of commensal enterobacteria from 310 healthy children living in Peru and Bolivia, using a metagenomic approach. Analysis of randomly selected enterobacterial pools revealed that qnrB was mainly carried by Escherichia coli and qnrS by Klebsiella pneumoniae. Investigation of 11 qnrB-positive isolates and 9 qnrS-positive isolates revealed the presence of plasmid-borne qnrB19 (n = 8), qnrB2 (n = 2), qnrB10 (n = 1), and qnrS1 (n = 9) genes.

Prevalence and molecular characterization of ampicillin-resistant Enterobacteriaceae isolated from traditional Egyptian Domiati cheese

The aim of this study was to address the prevalence and the molecular characteristics of antibiotic-resistant enteric bacteria isolated from one of the most popular types of Egyptian cheese. A total of 215 ampicillin-resistant enterobacterial isolates were obtained from 80 samples of Domiati cheese, and they were screened by PCR for a large pool of antibiotic resistance markers, including extended-spectrum beta-lactamases (ESBLs), class 1 and class 2 integrons, and plasmid-mediated quinolone resistance genes. It was determined that the most frequent mechanism of ampicillin resistance was from a TEM-1-type beta-lactamase. As well, SHV beta-lactamases, including SHV-1, SHV-25, and SHV-26, showed a high prevalence, and two novel SHV beta-lactamases, SHV-110 and SHV-111, were identified. Type CTX-M-14, OXY-1, OXA-1, and CMY-4 beta-lactamases were also detected in a few isolates. In addition, a novel AmpC beta-lactamase was detected that was designated CMY-41. Sequencing results of class 1 integrons revealed that the uncommon aminoglycoside resistance gene cassette aadA22 was found for the first time in an Escherichia coli strain. The other class 1 integrons harbored various common gene cassettes, including aadA1, aadA1a, aadA2, aadA12, dfr5, dfr7, dfr12, and dfr15. The only isolate that carried a class 2 integron contained dfrA1, sat2, and aadA1. Plasmid-mediated quinolone resistance determinants qnrS and qnrB showed a low prevalence. This study provides meaningful data on high antimicrobial resistance contained in Domiati cheese samples and reports for the first time the presence of beta-lactamases, plasmid-mediated quinolone resistance, and integrons in isolates from food of Egyptian animal origin.

Characterization of Salmonella enterica isolates from infants and toddlers in Wuhan, China

BACKGROUND

Extended-spectrum cephalosporins and fluoroquinolones are important antimicrobials for treating invasive salmonellosis, and emerging resistance to these antimicrobials is of paramount concern. This study reports on the antimicrobial susceptibility and molecular characterization of Salmonella enterica isolates recovered in 2006 from 0- to 3-year-old outpatients in China.

METHODS

The isolates were subjected to serotyping, antimicrobial susceptibility testing, screening for beta-lactamase genes, mutations in the quinolone resistance determining regions (QRDRs), qnr alleles and aac-(6')-Ib-cr by PCR followed by DNA sequence analysis. All Salmonella Typhimurium isolates and 43 selected non-Typhimurium isolates were further characterized by PFGE to determine the genetic relatedness.

RESULTS

From 3746 paediatric outpatient stool samples, 221 (5.9%) S. enterica isolates of 29 distinct serotypes were recovered. The antimicrobial resistance profiles differed among serotypes. Ciprofloxacin-resistant isolates were concentrated in serotype Typhimurium that were resistant to at least four additional non-quinolone antimicrobials. Nineteen out of 22 ciprofloxacin-resistant Salmonella Typhimurium isolates were grouped into one PFGE cluster. Plasmid-mediated quinolone resistance determinant aac-(6')-Ib-cr was detected in 18 S. enterica isolates and 4 isolates also carried qnr alleles. Plasmid-mediated blaCTX-M-14-like genes were found in seven ceftriaxone-resistant isolates, and two isolates also exhibited reduced susceptibility to ciprofloxacin.

CONCLUSIONS

Based on these results, fluoroquinolones should not be used to treat the invasive Salmonella Typhimurium infections in this local community. The monitoring programme should stay vigilant for ceftriaxone-resistant S. enterica isolates with reduced fluoroquinolone susceptibility.