Genetic relatedness and virulence potential of Salmonella Schwarzengrund strains with or without an IncFIB-IncFIC(FII) fusion plasmid isolated from food and clinical sources

A total of 55 food and clinical S. Schwarzengrund isolates were assayed for plasmid content, among which an IncFIB-IncFIC(FII) fusion plasmid, conferring streptomycin resistance, was detected in 17 isolates. Among the 17 isolates, 9 were food isolates primarily collected from poultry meat, and 8 clinical isolates collected from stool, urine, and gallbladder. SNP-based phylogenetic analyses showed that the isolates carrying the fusion plasmid formed a subclade indicating the plasmid was acquired and is now maintained by the lineage. Phylogenetic analysis of the plasmid suggested it is derived from avian pathogenic plasmids and might confer an adaptive advantage to the S. Schwarzengrund isolates within birds. IncFIB-IncFIC(FII) fusion plasmids from all food and three clinical isolates were self-conjugative and successfully transferred into E. coli J53 by conjugation. Food and clinical isolates had similar virulome profiles and were able to invade human Caco-2 cells. However, the IncFIB-IncFIC(FII) plasmid did not significantly add to their invasion and persistence potential in human Caco-2 cells.

Benzalkonium chloride forces selective evolution of resistance towards antibiotics in Salmonella enterica serovar Typhimurium

BACKGROUND

Although food-grade disinfectants are extensively used worldwide, it has been reported that the long-term exposure of bacteria to these compounds may represent a selective force inducing evolution including the emergence of antibiotic resistance. However, the mechanism underlying this correlation has not been elucidated. This study aims to investigate the genomic evolution caused by long-term disinfectant exposure in terms of antibiotic resistance in Salmonella enterica Typhimurium.

METHODS

S. Typhimurium isolates were exposed to increasing concentrations of benzalkonium chloride (BAC) and variations of their antibiotic susceptibilities were monitored. Strains that survived BAC exposure were analyzed at whole genome perspective using comparative genomics, and Sanger sequencing-confirmed mutations in ramR gene were identified. Next, the efflux activity in ramR-mutated strains shown as bisbenzimide accumulation and expression of genes involved in AcrAB-TolC efflux pump using quantitative reverse transcriptase PCR were determined.

RESULTS

Mutation rates of evolved strains varied from 5.82 × 10-9 to 5.56 × 10-8, with fold increase from 18.55 to 1.20 when compared with strains evolved without BAC. Mutations in ramR gene were found in evolved strains. Upregulated expression and increased activity of AcrAB-TolC was observed in evolved strains, which may contribute to their increased resistance to clinically relevant antibiotics. In addition, several indels and point mutations in ramR were identified, including L158P, A37V, G42E, F45L, and R46H which have not yet been linked to antimicrobial resistance. Resistance and mutations were stable after seven consecutive cultivations without BAC exposure. These results suggest that strains with sequence type (ST) ST34 were the most prone to mutations in ramR among the three STs tested (ST34, ST19, ST36).

CONCLUSIONS

This work demonstrated that disinfectants, specifically BAC forces S. Typhimurium to enter a specific evolutionary trajectory towards antibiotic resistance illustrating the side effects of long-term exposure to BAC and probably also to other disinfectants. Most significantly, this study provides new insights in understanding the emergence of antibiotic resistance in modern society.

Antibiotic Resistance in Non-Typhoidal Salmonella enterica Strains Isolated from Chicken Meat in Indonesia

The increase in antibiotic resistance in non-typhoidal Salmonella enterica (NTS) has been confirmed in Indonesia by this study. We confirmed the virulence genes and antimicrobial susceptibilities of clinical NTS (n = 50) isolated from chicken meat in Indonesia and also detected antimicrobial resistance genes. Of 50 strains, 30 (60%) were non-susceptible to nalidixic acid (NA) and all of them had amino acid mutations in gyrA. Among 27 tetracycline (TC) non-susceptible strains, 22 (81.5%) had tetA and/or tetB. The non-susceptibility rates to ampicillin, gentamicin or kanamycin were lower than that of NA or TC, but the prevalence of blaTEM or aadA was high. Non-susceptible strains showed a high prevalence of virulence genes compared with the susceptible strains (tcfA, p = 0.014; cdtB, p < 0.001; sfbA, p < 0.001; fimA, p = 0.002). S. Schwarzengrund was the most prevalent serotype (23 strains, 46%) and the most frequently detected as multi-antimicrobial resistant. The prevalence of virulence genes in S. Schwarzengrund was significantly higher than other serotypes in hlyE (p = 0.011) and phoP/Q (p = 0.011) in addition to the genes above. In conclusion, NTS strains isolated from Indonesian chicken had a high resistance to antibiotics and many virulence factors. In particular, S. Schwarzengrund strains were most frequently detected as multi-antimicrobial resistant and had a high prevalence of virulence genes.

Emergence of ciprofloxacin heteroresistance in foodborne Salmonella enterica serovar Agona

BACKGROUND

Bacterial heteroresistance has been increasingly identified as an important phenomenon for many antibiotic/bacterium combinations.

OBJECTIVES

To investigate ciprofloxacin heteroresistance in Salmonella and characterize mechanisms contributing to ciprofloxacin heteroresistance.

METHODS

Ciprofloxacin-heteroresistant Salmonella were identified by population analysis profiling (PAP). Target mutations and the presence of PMQR genes were detected using PCR and sequencing. Expression of acrB, acrF and qnrS was conducted by quantitative RT-PCR. Competition ability and virulence were also compared using pyrosequencing, blue/white screening, adhesion and invasion assays and a Galleria model. Two subpopulations were whole-genome sequenced using Oxford Nanopore and Illumina platforms.

RESULTS

PAP identified one Salmonella from food that yielded a subpopulation demonstrating heteroresistance to ciprofloxacin at a low frequency (10-9 to 10-7). WGS and PFGE analyses confirmed that the two subpopulations were isogenic, with six SNPs and two small deletions distinguishing the resistant from the susceptible. Both subpopulations possessed a T57S substitution in ParC and carried qnrS. The resistant subpopulation was distinguished by overexpression of acrB and acrF, a deletion within rsxC and altered expression of soxS. The resistant population had a competitive advantage against the parental population when grown in the presence of bile salts but was attenuated in the adhesion and invasion of human intestinal cells.

CONCLUSIONS

We determined that heteroresistance resulted from a combination of mutations in fluoroquinolone target genes and overexpression of efflux pumps associated with a deletion in rsxC. This study warns that ciprofloxacin heteroresistance exists in Salmonella in the food chain and highlights the necessity for careful interpretation of antibiotic susceptibility.

Antimicrobial resistance and virulence factors profile of Salmonella spp. and Escherichia coli isolated from different environments exposed to anthropogenic activity

OBJECTIVE

The study aimed to identify the antimicrobial resistance (AMR) determinants and virulence factors in Salmonella spp. and Escherichia coli recovered from different anthropogenic areas in North Carolina.

METHODS

Soil samples were collected from different anthropogenic areas, urban and natural. The minimum inhibitory concentration (MIC) was determined by using the broth microdilution method. Whole-genome sequencing (WGS) and analysis were done to identify the AMR determinants and virulence factors.

RESULTS

A higher prevalence of Salmonella spp. and E. coli was detected in the urban environment. The Salmonella spp. isolates showed resistance to sulfisoxazole and streptomycin, whereas E. coli was resistant to sulfisoxazole, cefoxitin and ampicillin. Salmonella serotypes Schwarzengrund and Mississippi were identified based on WGS analysis. Aminoglycoside resistance genes and IncFIB and IncFIC(FII) plasmids were detected among Salmonella spp. In general, E. coli was predominated by isolates from phylogroups B1, B2 and D. The multidrug transporter mdfA gene was detected in most of the E. coli from both the urban (100%) and natural (84.5%) environments. The FosA7 gene was detected in an isolate from a residential yard. The pCoo and pB171 plasmids were detected in an urban environment; col(156) and pHN7A8 plasmids were detected in natural environments.

CONCLUSIONS

The detection of AMR determinants and virulence factors in these bacteria is significant in understanding the occurrence and even the development of AMR. The presence of these determinants in different anthropogenic areas suggests the need to conduct longitudinal studies for comparing the profile of pathogens across different environments.

Circulation of Plasmids Harboring Resistance Genes to Quinolones and/or Extended-Spectrum Cephalosporins in Multiple Salmonella enterica Serotypes from Swine in the United States

Nontyphoidal Salmonella enterica (NTS) poses a major public health risk worldwide that is amplified by the existence of antimicrobial-resistant strains, especially those resistant to quinolones and extended-spectrum cephalosporins (ESC). Little is known on the dissemination of plasmids harboring the acquired genetic determinants that confer resistance to these antimicrobials across NTS serotypes from livestock in the United States. NTS isolates (n = 183) from U.S. swine clinical cases retrieved during 2014 to 2016 were selected for sequencing based on their phenotypic resistance to enrofloxacin (quinolone) or ceftiofur (3rd-generation cephalosporin). De novo assemblies were used to identify chromosomal mutations and acquired antimicrobial resistance genes (AARGs). In addition, plasmids harboring AARGs were identified using short-read assemblies and characterized using a multistep approach that was validated by long-read sequencing. AARGs to quinolones [qnrB15, qnrB19, qnrB2, qnrD, qnrS1, qnrS2, and aac(6')Ib-cr] and ESC (bla _CMY-2, bla _CTX-M-1, bla _CTX-M-27, and bla _SHV-12) were distributed across serotypes and were harbored by several plasmids. In addition, chromosomal mutations associated with resistance to quinolones were identified in the target enzyme and efflux pump regulation genes. The predominant plasmid harboring the prevalent qnrB19 gene was distributed across serotypes. It was identical to a plasmid previously reported in S. enterica serovar Anatum from swine in the United States (GenBank accession number KY991369.1) and similar to Escherichia coli plasmids from humans in South America (GenBank accession numbers GQ374157.1 and JN979787.1). Our findings suggest that plasmids harboring AARGs encoding mechanisms of resistance to critically important antimicrobials are present in multiple NTS serotypes circulating in swine in the United States and can contribute to resistance expansion through horizontal transmission.

Draft Genome Sequences of 27 Salmonella enterica Serovar Schwarzengrund Isolates from Clinical Sources

Twenty-seven Salmonella enterica serovar Schwarzengrund isolates from clinical sources were sequenced as part of a larger study to examine phenotypic and genotypic characteristics. The majority of the sequenced strains were isolated from human stool (n = 20) followed by urine (n = 3) and blood (n = 2).

Twenty-seven Salmonella enterica serovar Schwarzengrund isolates from clinical sources were sequenced as part of a larger study to examine phenotypic and genotypic characteristics. The majority of the sequenced strains were isolated from human stool (n = 20) followed by urine (n = 3) and blood (n = 2). Four isolate sequences contained plasmids of known incompatibility groups.

Association of Salmonella Serotypes with Quinolone Resistance in Broilers

Fluoroquinolone is widely used for the treatment of bacterial diseases, and the emergence of quinolone resistance has become a serious concern in recent years, owing to an increase and inappropriate use of antimicrobials. Here, we attempted to understand the differences in the emergence frequency of quinolone-resistant bacterial variants in three Salmonella serotypes S. Infantis, S. Schwarzengrund, and S. Manhattan—which are mainly found in broiler industries in Japan. Emergence frequency tests for quinolone-resistant variants using enrofloxacin-containing agar plates and sequence analysis in the quinolone resistance-determining region (QRDR) of gyrA in DNA gyrase were performed. The results showed no significant difference in the emergence frequency among the three serotypes, and most of the resistant variants had mutations in the QRDR region. These findings suggest that differences in the serotypes tested are not associated with the emergence frequency of quinolone-resistant variants.

Draft Genome Sequences of Ciprofloxacin-Resistant Salmonella enterica Strains with Multiple-Antibiotic Resistance, Isolated from Imported Foods

We report here the draft genome sequences of 15 ciprofloxacin-resistant Salmonella enterica strains with resistance to multiple other antibiotics, including aminoglycosides, β-lactams, sulfonamides, tetracycline, and trimethoprim, isolated from different imported foods. Three strains (NCTR75, NCTR281, and NCTR350) showed a high level of ciprofloxacin resistance compared to that of the other isolates. The whole-genome sequencing data provide a better understanding of the antibiotic resistance mechanisms and virulence properties of these isolates.

Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella enterica

Antimicrobial resistance (AMR) in pathogenic microorganisms with multidrug resistance (MDR) constitutes a severe threat to human health. A major causative mechanism of AMR is mediated through the multidrug efflux pump (MEP). The resistance-nodulation-division superfamily (RND family) of Gram-negative bacteria is usually the major cause of MDR in clinical studies. In Salmonella enterica, the RND pump is translated from the acrAB gene, which is regulated by the activator RamA. Many MEP-caused AMR strains have high ramA gene expression due to mutations in RamR, which has a homodimeric structure comprising the dimerization domain and DNA-binding domain (DBD). Three mutations on the dimerization domain, namely Y59H, M84I, and E160D, are far from the DBD; the molecular mechanism through which they influence RamR’s binding affinity to the ramA gene promoter and consequently disrupt RamA remains unclear. The present study conducted molecular dynamics simulations, binding free energy calculations, and normal mode analysis to investigate the mechanism through which Y59H, M84I, and E160D mutations on the dimerization domain influence the binding affinity of RamR to the ramA promoter. The present results suggest that the three mutations alter the RamR structure, resulting in decreased DNA-binding affinity.

The effects of different enrofloxacin dosages on clinical efficacy and resistance development in chickens experimentally infected with Salmonella Typhimurium

To investigate the optimal dosage which can improve clinical efficacy and minimize resistance, pharmacokinetics/pharmacodynamics model of enrofloxacin was established. Effect of enrofloxacin treatments on clearance of Salmonella in experimentally infected chickens and simultaneously resistance selection in Salmonella and coliforms were evaluated in three treatment groups (100, PK/PD designed dosage of 4, 0.1 mg/kg b.w.) and a control group. Treatment duration was three rounds of 7-day treatment alternated with 7-day withdrawal. Results showed that 100 mg/kg b.w. of enrofloxacin completely eradicated Salmonella, but resistant coliforms (4.0-60.8%) were selected from the end of the second round's withdrawal period till the end of the experiment (days 28-42). PK/PD based dosage (4 mg/kg b.w.) effectively reduced Salmonella for the first treatment duration. However upon cessation of medication, Salmonella repopulated chickens and persisted till the end with reduced susceptibility (MICCIP = 0.03-0.25 mg/L). Low frequency (5-9.5%) of resistant coliforms was selected (days 39-42). Enrofloxacin at dosage of 0.1 mg/kg b.w. was not able to eliminate Salmonella and selected coliforms with slight decreased susceptibility (MICENR = 0.25 mg/L). In conclusion, short time treatment (7 days) of enrofloxacin at high dosage (100 mg/kg b.w.) could be effective in treating Salmonella infection while minimizing resistance selection in both Salmonella and coliforms.

Population dynamics and antimicrobial resistance of the most prevalent poultry-associated Salmonella serotypes

Salmonella spp. is the most predominant bacterial cause of foodborne gastroenteritis in humans. Due to the risk of human infection associated with poultry products and the prevalence of antimicrobial resistance, Salmonella also poses a significant challenge to commercial poultry production. During the last decade (2002 to 2012), the 12 most prevalent poultry-associated Salmonella serotypes (MPPSTs) were frequently and consistently isolated from poultry products in the United States. These MPPSTs and their percent prevalence in poultry products include Kentucky (4%), Enteritidis (2%) Heidelberg (2%), Typhimurium (2%), S. I 4,[5],12:i:- (0.31%), Montevideo (0.20%), Infantis (0.16%) Schwarzengrund (0.15%), Hadar (0.15%), Mbandaka (0.13%), Thompson (0.12%), and Senftenberg (0.04%). All MPPSTs except Kentucky are among the top 30 clinically significant serotypes that cause human illnesses in the United States. However with the exception of a few widely studied serotypes such as S. Enteritidis and Typhimurium, the ecology and epidemiology of the majority of MPPSTs still remain poorly investigated. Published data from the United States suggests that MPPSTs such as Heidelberg, Typhimurium, Kentucky, and Sentfenberg are more likely to be multi-drug resistant (MDR, ≥3 antimicobial classes) whereas Enteritidis, Montevideo, Schwarzengrund, Hadar, Infantis, Thompson, and Mbandaka are generally pan-susceptible or display resistance to fewer antimicobials. In contrast, the majority of MPPSTs isolated globally have been reported to display MDR phenotype. There also appears to be an international spread of a few MDR serotypes including Kentucky, Schwarzengrund, Hadar, Thomson, Sentfenberg, and Enteritidis, which may pose significant challenges to the public health. The current knowledge gaps on the ecology, epidemiology, and antimicrobial resistance of MPPSTs are discussed.

Resistance mechanisms and fitness of Salmonella Typhimurium and Salmonella Enteritidis mutants evolved under selection with ciprofloxacin in vitro

The aim of this study was to investigate the difference in resistance mechanisms and fitness of Salmonella Typhimurium (ST) and Salmonella Enteritidis (SE) mutants selected during the evolution of resistance under exposure to increasing ciprofloxacin concentrations in vitro. Mutations in quinolone target genes were screened by PCR. Phenotypic characterization included susceptibility testing by the broth dilution method, investigation of efflux activity and growth rate, and determination of the invasion of human intestinal epithelium cells in vitro. The two Salmonella serotypes exhibited differences in target gene mutations and efflux pump gene expression during the development of resistance. In the parental strains, ST had a competitive advantage over SE. During the development of resistance, initially, the SE strain was more competitive. However, once ciprofloxacin resistance was acquired, ST once again became the more competitive strain. In the absence of bile salts or at 0.1% bile, the growth rate of SE was initially greater than that of ST, but once ciprofloxacin resistance was acquired, ST had higher growth rates. ST strains showed decreased invasion of epithelial cells in 0.1% bile. These data indicate that ciprofloxacin-resistant ST strains are more competitive than ciprofloxacin-resistant SE strains.

Roles of ramR and tet(A) Mutations in Conferring Tigecycline Resistance in Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

Tigecycline is regarded as a last-resort treatment for carbapenem-resistant Klebsiella pneumoniae (CRKP) infections, but increasing numbers of tigecycline-resistant K. pneumoniae isolates have been reported. The tigecycline resistance mechanisms in CRKP are undetermined. This study aimed to elucidate the mechanisms underlying tigecycline resistance in 16 tigecycline- and carbapenem-resistant K. pneumoniae (TCRKP) isolates. Mutations in tigecycline resistance determinant genes [ramR, acrR, oqxR, tet(A), tet(L), tet(X), tet(M), rpsJ] were assessed by PCR amplicon sequencing, and mutations in ramR and tet(A) exhibited high prevalences individually (81%) and in combination (63%). Eight functional ramR mutation profiles reducing tigecycline sensitivity were verified by plasmid complementation of wild-type and mutant ramR Using a site-specific mutant, the most frequent RamR mutation, A19V (60%), had no significant effect on tigecycline susceptibility or the upregulation of ramA and acrA Two tet(A) variants with double frameshift mutations, type 1 and type 2, were identified; type 2 tet(A) is novel. A parent strain transformed with a plasmid carrying type 1 or type 2 tet(A) increased the tigecycline MIC by 8-fold or 4-fold, respectively. Synergistic effects were observed in strains harboring no ramR gene and a mutated tet(A), with an 8-fold increase in the tigecycline MIC compared with that in strains harboring only mutated tet(A) being seen. Overall, mutations in the ramR and tet(A) efflux genes constituted the major tigecycline resistance mechanisms among the studied TCRKP isolates. The identification of strains exhibiting the combination of a ramR deficiency and widespread mutated tet(A) is concerning due to the possible dissemination of increased tigecycline resistance in K. pneumoniae.

Genotypic relatedness and antimicrobial resistance of Salmonella Heidelberg isolated from chickens and turkeys in the midwestern United States

Salmonella is one of the most common causes of foodborne illnesses in humans in the United States, and domestic poultry is considered an important source of this pathogen. Salmonella enterica subsp. enterica serovar Heidelberg is the fourth most commonly reported Salmonella from retail meats and food animals in the United States. We assessed the genotypes and antimicrobial resistance phenotypes of Salmonella Heidelberg isolated from various chicken and turkey hatcheries and breeder farms in the Midwest. The genotypes of 33 S. Heidelberg isolates from chickens ( n = 19) and turkeys ( n = 14) were compared using pulsed-field gel electrophoresis analysis. Cluster analysis of the fingerprints showed that the majority of the chicken isolates grouped together with 87% similarity; those from turkeys clustered with 88% similarity. Similarity between chicken and turkey isolates was also high (86%). Isolates from turkeys were generally more genetically diverse than those from chickens. Antimicrobial susceptibility analysis detected resistance to sulfisoxazole (36% of the isolates), streptomycin (33%), gentamicin (27%), tetracycline (24%), ampicillin and amoxicillin-clavulanic acid (15%), cefoxitin (12%), ceftriaxone and ceftiofur (12%), and chloramphenicol (9%). None of the isolates was resistant to azithromycin, ciprofloxacin, or nalidixic acid. Although the number of the isolates was limited in our study, we conclude that S. Heidelberg isolates from the same host generally clustered together and that a considerable number of the isolates were resistant to a number of antimicrobial agents.

Isolation and Characterization of Antimicrobial-Resistant Nontyphoidal Salmonella enterica Serovars from Imported Food Products

The objective of this study was to determine antimicrobial resistance and elucidate the resistance mechanism in nontyphoidal Salmonella enterica serovars isolated from food products imported into the United States from 2011 to 2013. Food products contaminated with antimicrobial-resistant nontyphoidal S. enterica were mainly imported from Taiwan, Indonesia, Vietnam, and China. PCR, DNA sequencing, and plasmid analyses were used to characterize antimicrobial resistance determinants. Twentythree of 110 S. enterica isolates were resistant to various antimicrobial classes, including β-lactam, aminoglycoside, phenicol, glycopeptide, sulfonamide, trimethoprim, and/or fluoroquinolone antimicrobial agents. Twelve of the isolates were multidrug resistant strains. Antimicrobial resistance determinants blaTEM-1, blaCTX-M-9, blaOXA-1, tetA, tetB, tetD, dfrA1, dfrV, dhfrI, dhfrXII, drf17, aadA1, aadA2, aadA5, orfC, qnrS, and mutations of gyrA and parC were detected in one or more antimicrobial-resistant nontyphoidal S. enterica strains. Plasmid profiles revealed that 12 of the 23 antimicrobial-resistant strains harbored plasmids with incompatibility groups IncFIB, IncHI1, IncI1, IncN, IncW, and IncX. Epidemiologic and antimicrobial resistance monitoring data combined with molecular characterization of antimicrobial resistance determinants in Salmonella strains isolated from imported food products may provide information that can be used to establish or implement food safety programs to improve public health.

First Description of the Extended Spectrum-Beta-Lactamase Gene blaCTX-M-109 in Salmonella Grumpensis Strains Isolated from Neonatal Nosocomial Infections in Dakar, Senegal

Nosocomial infections are very common in African hospitals, particularly in neonatal units. These infections are most often caused by bacteria such as Escherichia coli, Klebsiella spp and Staphylococcus spp. Salmonella strains are rarely involved in nosocomial infections. Here, we report the first description of S. Grumpensis in neonatal infections in Senegal. Seventeen Salmonella strains were isolated from hospitalized infants' stool samples. The following resistance phenotype was described in strains: AMXRTICRCFR FOXRCFXRCTXRCAZRIMPSATMRNARNORRCIPRTMRGMRTERSXTR. All isolates were susceptible to imipenem, 15 out of 17 produced an extended spectrum ß-lactamase (ESBL). blaOXA-1, blaSHV-1, blaTEM-1, blaCTX-M1 genes were detected in strains 8, 13, 5 and 8, respectively. blaCTX-M1 sequencing revealed the presence of blaCTX-M-109. Thirteen of the 17 Salmonella Grumpensis strains were analyzed by PFGE. These 13 isolates belonged to a single pulsotype and were genotypically identical. This is the first report of neonatal S. Grumpensis infections in Senegal, and the first report of blaCTX-M-109 in the genus Salmonella.

Characterization of extended-spectrum β-lactamase (ESBL) producing non-typhoidal Salmonella (NTS) from imported food products

Food contaminated with extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica has emerged as an important global issue due to the international food-product trade. Therefore, the purpose of this study was to investigate whether imported food products can serve as a reservoir for non-typhoidal Salmonella (NTS) that can transmit β-lactam-resistance to humans through ingestion of the contaminated food. NTS isolates (n=110) were collected from various imported food products (n=3480) from 2011 to 2013. The NTS isolates were analyzed by serotyping, antimicrobial susceptibility tests, and plasmid profiling. Salmonella ser. Weltevreden, Salmonella ser. Newport, Salmonella ser. Senftenberg, Salmonella ser. Virchow, Salmonella ser. Enteritidis, Salmonella ser. Typhimurium, and Salmonella ser. Bareilly were the most prevalent serovars. Nine NTS strains were resistant to ampicillin and/or one or more cephalosporins (MIC>32 μg/mL). Polymerase chain reaction (PCR) detection revealed that all nine isolates carried the bla(TEM-1) β-lactamase gene, with or without the bla(CTX-M-9) or bla(OXA-1) genes. Two isolates, PSS_913 and PSS_988, exhibited decreased susceptibility to extended-spectrum cephalosporins and ampicillin. Plasmids ranging in size from less than 8 to over 165 kbp, from all of the 9 resistant isolates, belonged to the IncHI1, IncI1, IncN, or IncX groups. Conjugation experiments and Southern hybridization, using bla(TEM-1), confirmed the plasmid-mediated transfer of ESBL genes, which resulted in increased MICs of β-lactams for Escherichia coli transconjugants. The contamination of imported food products by NTS with conjugative plasmid-borne ESBL genes may contribute to the spread of ESBL-producing NTS and compromise the therapeutic activity of extended-spectrum β-lactam antibiotics.

Serotypes and antimicrobial susceptibility of Salmonella spp. isolated from farm animals in China

Salmonella spp. can indirectly infect humans via transfer from animals and animal-derived food products, and thereby cause potentially fatal diseases. Therefore, gaining an understanding of Salmonella infection in farm animals is increasingly important. The aim of this study was to identify the distribution of serotypes in Salmonella samples isolated from chickens (n = 837), pigs (n = 930), and dairy cows (n = 418) in central China (Henan, Hubei, and Hunan provinces) in 2010-2011, and investigate the susceptibility of strains to antimicrobial agents. Salmonella isolates were identified by PCR amplification of the invA gene, serotypes were determined by using a slide agglutination test for O and H antigens, and susceptibility to 24 antimicrobials was tested using the agar dilution method. In total, 248 Salmonella strains were identified: 105, 105, and 38 from chickens, dairy cows, and pigs, respectively. Additionally, 209 strains were identified in diseased pigs from the Huazhong Agricultural University veterinary hospital. Among these 457 strains, the dominant serotypes were Typhimurium in serogroup B, IIIb in serogroup C, and Enteritidis in serogroup D. In antimicrobial susceptibility tests, 41.14% of Salmonella spp. were susceptible to all antimicrobial agents, 48.14% were resistant to at least one, and 34.72% were resistant to more than three classes. Strains were highly resistant to sulfamethoxazole-trimethoprim (39.61%), nalidixic acid (39.17%), doxycycline (28.22%), and tetracycline (27.58%). Resistance to cephalosporins and fluoroquinolones ranged from 5.25 to 7.44% and 19.04 to 24.51%, respectively. Among penicillin-resistant and cephalosporin-resistant strains, 25 isolates produced extended-spectrum β-lactamases (ESBLs). The multidrug-resistant and ESBL-producing Salmonella strains identified in healthy animals here will present a challenge for veterinary medicine and farm animal husbandry, and could also pose a threat to public health. The level of antibiotic resistance observed in this study further highlights the need for careful and selective use of antibiotics.

Detection and functionality of the CdtB, PltA, and PltB from Salmonella enterica serovar Javiana

Salmonella infection is one of the major foodborne illnesses in the United States. Several Gram-negative bacterial pathogens, including Salmonella Typhi, produce cytolethal distending toxin (CDT), which arrests growth, induces apoptosis of infected host cells and extends persistence of pathogenic bacteria in the host. The aim of this study was to characterize the functionality of CDT (cdtB, pltA and pltB) from nontyphoidal Salmonella isolates. Fifty Salmonella enterica serovar Javiana isolates from food, environmental, and clinical samples were screened for cdtB, pltA, and pltB genes by PCR, and all were positive for all three genes. Nucleotide sequence analysis of all amplified PCR products showed 100% identity to S. Typhi cdtB. To understand the roles of CdtB, PltA, and PltB in S. Javiana, cdtB, pltA, and pltB deletion mutants were constructed using a lambda Red-based recombination system. In vitro-cultured HeLa cell lines were infected with a wild-type strain and its isogenic ∆cdtB, ∆pltA, and ∆pltB to determine whether the strains of S. Javiana are responsible for invasion and cytolethal distending intoxication, including cell cycle arrest, cytoplasmic distension, and nuclear enlargement of host target cells. The results showed that HeLa cells infected with S. Javiana wild type were arrested in G2 /M and had distended cytoplasm and nuclei that were larger than those infected with S. Javiana ∆cdtB and ∆pltA strains. The S. Javiana ∆pltB strain retained the ability to induce cytoplasmic distension and cell cycle arrest, whereas the complemented ∆cdtB and ∆pltA S. Javiana strains showed activity like the wild-type strains. CdtB and pltA from S. Javiana had apparent effects on the distension of both cytoplasm and nucleus as well as cell cycle arrest of HeLa cell lines after 72 h of infection. Our data show a significant difference between the wild-type cdtB strain and its isogenic ∆cdtB for invasion of the cell lines. Therefore, CdtB produced from S. Javiana strains may play an important role in pathogenesis in host cells.

Lack of efflux mediated quinolone resistance in Salmonella enterica serovars Typhi and Paratyphi A

Salmonella enterica serovars Typhi and Paratyphi A isolates from human patients in France displaying different levels of resistance to quinolones or fluoroquinolones were studied for resistance mechanisms to these antimicrobial agents. All resistant isolates carried either single or multiple target gene mutations (i.e., in gyrA, gyrB, or parC) correlating with the resistance levels observed. Active efflux, through upregulation of multipartite efflux systems, has also been previously reported as contributing mechanism for other serovars. Therefore, we investigated also the occurrence of non-target gene mutations in regulatory regions affecting efflux pump expression. However, no mutation was detected in these regions in both Typhi and Paratyphi isolates of this study. Besides, no overexpression of the major efflux systems was observed for these isolates. Nevertheless, a large deletion of 2334 bp was identified in the acrS-acrE region of all S. Typhi strains but which did not affect the resistance phenotype. As being specific to S. Typhi, this deletion could be used for specific molecular detection purposes. In conclusion, the different levels of quinolone or FQ resistance in both S. Typhi and S. Paratyphi A seem to rely only on target modifications.

The crystal structure of multidrug-resistance regulator RamR with multiple drugs

RamR is a transcriptional repressor of the gene-encoding RamA protein, which controls the expression of the multidrug efflux system genes acrAB-tolC. RamR is an important multidrug-resistance factor, however, its structure and the identity of the molecules to which it responds have been unknown. Here, we report the crystal structure of RamR in complex with multiple drugs, including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6G. All compounds are found to interact with Phe155 of RamR, and each compound is surrounded by different amino acid residues. Binding of these compounds to RamR reduces its DNA-binding affinity, which results in the increased expression of ramA. Our results reveal significant flexibility in the substrate-recognition region of RamR, which regulates the bacterial efflux participating in multidrug resistance.

ramR mutations affecting fluoroquinolone susceptibility in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198

A screening for non-target mutations affecting fluoroquinolone susceptibility was conducted in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198. Among a panel of representative isolates (n = 27), covering the epidemic, only three showed distinct mutations in ramR resulting in enhanced expression of genes encoding the AcrAB-TolC efflux system and low increase in ciprofloxacin MIC. No mutations were detected in other regulatory regions of this efflux system. Ciprofloxacin resistance in serovar Kentucky ST198 is thus currently mainly due to multiple target gene mutations.

The tetA gene decreases tigecycline sensitivity of Salmonella enterica isolates

To determine the association of tetracycline resistance determinants with tigecycline sensitivity, tetracycline-resistant Salmonella spp. isolated from clinical and food samples were tested for the presence of tetracycline resistance determinants, tigecycline sensitivity, and the impact of tetA on tigecycline resistance. In addition, the impacts of multiple resistance mechanisms on tigecycline resistance were determined using an isolate with ramR mutation. Of the 49 tetracycline-resistant Salmonella isolates screened, 32 were positive for tetA, 13 were positive for tetB, 2 were positive for tetC and 1 isolate was positive for both tetA and tetB. The minimum inhibitory concentration (MIC) of tigecycline for tetA-carrying isolates ranged from 0.19 mg/L to 3mg/L (mode 0.75 mg/L), whereas the MIC of tigecycline for tetB-carrying isolates ranged from 0.064 mg/L to 0.5mg/L (modes 0.25mg/L and 0.38 mg/L, excluding the isolate with both tetA and tetB). Double frameshift mutations in codons 201, 202 and 203 were observed in partial sequences of the tetA genes in these strains and the majority of published tetA gene sequences. Curing of the tetA genes from three isolates reduced the tigecycline MICs, whilst deletion of ramR increased tigecycline MICs. This study indicates that the tetA gene decreases sensitivity to tigecycline in Salmonella spp. at a low level. With additional resistance mechanisms, tetA-carrying strains can reach the breakpoint for tigecycline resistance.

Marine sediment bacteria harbor antibiotic resistance genes highly similar to those found in human pathogens

The ocean is a natural habitat for antibiotic-producing bacteria, and marine aquaculture introduces antibiotics into the ocean to treat infections and improve aquaculture production. Studies have shown that the ocean is an important reservoir of antibiotic resistance genes. However, there is a lack of understanding and knowledge about the clinical importance of the ocean resistome. We investigated the relationship between the ocean bacterial resistome and pathogenic resistome. We applied high-throughput sequencing and metagenomic analyses to explore the resistance genes in bacterial plasmids from marine sediments. Numerous putative resistance determinants were detected among the resistance genes in the sediment bacteria. We also found that several contigs shared high identity with transposons or plasmids from human pathogens, indicating that the sediment bacteria recently contributed or acquired resistance genes from pathogens. Marine sediment bacteria could play an important role in the global exchange of antibiotic resistance.

Molecular characterisation of quinolone resistance in Escherichia coli from animals in Turkey

The aim of this study were to detect the gyrA, parC and marR mutations and qnr genes (qnrA, qnrB and qnrS) in 120 strains of Escherichia coli isolated from animals. European Committee on Antimicrobial Susceptibility Testing and Clinical Laboratory Standards Institute disc diffusion and minimum inhibitory concentration (MIC) tests, respectively, were used to determine fluoroquinolone (FQ) resistance, and molecular methods were used to detect the mutations and the genes. E coli isolates with an MIC of ≥8&emsp14;mg/l had mutation at Ser-80 in parC in addition to mutations at Ser-83, Asp-87 or both in gyrA. The nucleotide change was detected in marR (Ser-3 → Asn, Ala-53 → Glu, Gly-103 → Ser, Tyr-137 → His). Only four E coli isolates (3.3 per cent) contained qnrA and qnrS, and qnrB was not detected. Two E coli isolates from healthy calves also contained qnrA and qnrS. The MICs of enrofloxacin and danofloxacin for qnr-containing E coli isolates ranged from 32&emsp14;mg/l to 256&emsp14;mg/l. The results of this study indicated that the FQ-resistant E coli isolates presented an alteration in gyrA (Ser-83 → Leu, Asp-87 → Asn) and parC (Ser-80 → Ile) with high MICs (8-256&emsp14;mg/l), and there was a low prevalence of qnr genes among E coli isolated from animals.