Enterica Isolates Research Articles

Detection of CTX-M-1 extended-spectrum beta-lactamase among ceftiofur-resistant Salmonella enterica clinical isolates of poultry.

Salmonella enterica resistance to extended-spectrum cephalosporins (ESC) conferred by cefotaximases (blaCTX-M) is a growing concern in the United States. Among food-producing animals, poultry are a major reservoir of ESC-resistant Salmonella. A retrospective study was carried out to further characterize 38 ceftiofur-resistant clinical Salmonella enterica isolates obtained from poultry during 2007-2018. Of the isolates tested, 31 displayed resistance to ceftriaxone and harbored blaCMY-2, whereas 7 isolates demonstrated resistance or reduced susceptibility to cefepime in addition to ceftriaxone resistance. These 7 isolates displayed extended-spectrum β-lactamase activity, harbored blaCTX-M-1, and were recovered only from recent poultry diagnostic submissions made in 2011-2018 as opposed to the 31 isolates that were recovered in 2007-2018. Further characterization of the blaCTX-M-1 gene determined that it was located on conjugative IncN/ST1 and IncI1/ST87 plasmids in the isolates from commercial turkeys and broilers, respectively. These plasmids have been responsible for extensive spread of blaCTX-M-1 in livestock, poultry, and humans in Europe. Potential transfer of IncN and IncI1 plasmids and/or nontyphoidal Salmonella carrying these plasmids through the food chain, or by other means to humans, may result in treatment failures. Our study demonstrates the importance of further characterization of ceftiofur-resistant S. enterica isolates detected by veterinary diagnostic laboratories to identify the sources of blaCTX-M-1 and to mitigate the spread of ESC-resistant Salmonella in the poultry production pyramid.

Prevalence, molecular characterization, and antimicrobial resistance profiles of Listeria monocytogenes, Salmonella enterica, and Escherichia coli O157:H7 on dairy cattle farms in Jordan

This study determined the prevalence, pulsed-field gel electrophoresis profiles, and antimicrobial resistance profile of Listeria monocytogenes, Salmonella enterica, and Escherichia coli O157:H7 isolates from dairy cattle farms in Jordan. Samples from bulk tank milk (n = 305), cattle feces (n = 610), and rectoanal mucosal swabs (n = 610) were collected from 61 dairy cattle farms. We confirmed 32 L. monocytogenes, 28 S. enterica, and 24 E. coli O157:H7 isolates from the samples. The farm-level prevalence (at least 1 positive sample per farm) of L. monocytogenes, S. enterica, and E. coli O157:H7 was 27.9, 19.7, and 23.0%, respectively. The prevalence of L. monocytogenes, S. enterica, and E. coli O157:H7 in bulk tank milk was 7.5, 1.6, and 3.3%, respectively. The prevalence of L. monocytogenes and S. enterica in fecal samples was 1.5 and 3.8%, respectively, and the prevalence of E. coli O157:H7 in rectoanal mucosal swabs was 2.3%. Based on disk diffusion testing, all L. monocytogenes, S. enterica, and E. coli O157:H7 isolates exhibited resistance to at least 1 antimicrobial class. Multidrug resistance (resistance to 3 or more classes of antimicrobials) was exhibited by 96.9% of L. monocytogenes, 91.7% of E. coli O157:H7, and 82.1% of S. enterica isolates. Moreover, 93.8, 79.2, and 57.1% of the L. monocytogenes, E. coli O157:H7, and S. enterica isolates, respectively, were resistant to 5 or more antimicrobial classes. More than 50% of L. monocytogenes isolates were resistant to ampicillin, clindamycin, penicillin, erythromycin, quinupristin-dalfopristin, streptomycin, teicoplanin, linezolid, vancomycin, kanamycin, and tetracycline. More than 50% of S. enterica and E. coli O157:H7 isolates were resistant to ampicillin, cephalothin, nalidixic acid, kanamycin, streptomycin, amoxicillin-clavulanic acid, and tetracycline. The prevalence of the studied pathogens this study was comparable to reports from other countries. The isolated pathogens exhibited a high degree of antimicrobial resistance, suggesting that the bacterial flora of dairy cattle in Jordan are under intense antimicrobial selection pressure. Additional research is required to determine the causes and drivers of resistance, and to develop approaches to mitigating antimicrobial resistance.

Comparative Genomics and Phenotypic Investigations Into Antibiotic, Heavy Metal, and Disinfectant Susceptibilities of Salmonella enterica Strains Isolated in Australia.

Salmonella enterica is recognized as a major contributor of gastrointestinal illness worldwide. Concerns have been raised over the increasing prevalence of antibiotic resistant strains of Salmonella isolated from animals and food, and the role of antibiotics and other antimicrobial agents such as biocides and heavy metals in the selection and dissemination of antibiotic resistant bacteria to human hosts. In this study the antibiotic, heavy metal and disinfectant resistance genotypes and phenotypes of 19 S. enterica isolates from food-producing animals were established using whole genome sequence analysis, disc diffusion, as well as broth or agar dilution methods. This study also investigated the genomic environment of resistance genes on mobile genetic elements and chromosomal DNA. An ampicillin and streptomycin resistant S. Infantis isolate in this study harbored a β-lactamase (blaTEM–1), and two streptomycin resistance conferring genes (strA and strB) on a class 1 integron mobilized on a large conjugative plasmid. This plasmid also harbored two arsenic resistance gene cassettes. The arsenic resistance cassette, arsRCDAB, was also observed in two S. Singapore isolates with high tolerance to arsenate. A nalidixic acid resistant S. Typhimurium isolate was found to possess a mutation in gyrA resulting in amino acid change Asp87Gly and tetracycline resistant S. Typhimurium isolate was found to harbor efflux pump gene, tetA. No resistance (genotypic or phenotypic) was recorded to the disinfectants screened in this study. Taken together, results of this study showed a good correlation between predicted and measured resistances when comparing genotypic and phenotypic data, respectively. The findings of this study do not suggest resistance to clinically relevant antibiotics are widespread among Salmonella isolated from Australian food-producing animals.

Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace.

Non-typhoidal Salmonella enterica serovars continue to be an important food safety issue worldwide. Cranberry (Vaccinium macrocarpon Ait) fruits possess antimicrobial properties due to their various acids and phenolic compounds; however, the underlying mechanism of actions is poorly understood. We evaluated the effects of cranberry extracts on the growth rate of Salmonella enterica serovars Typhimurium, Enteritidis and Heidelberg and on the transcriptomic profile of Salmonella Enteritidis to gain insight into phenotypic and transcriptional changes induced by cranberry extracts on this pathogen. An ethanolic extract from cranberry pomaces (KCOH) and two of its sub-fractions, anthocyanins (CRFa20) and non-anthocyanin polyphenols (CRFp85), were used. The minimum inhibitory (MICs) and bactericidal (MBCs) concentrations of these fractions against tested pathogens were obtained using the broth micro-dilution method according to the Clinical Laboratory Standard Institute’s guidelines. Transcriptional profiles of S. Enteritidis grown in cation-adjusted Mueller-Hinton broth supplemented with or without 2 or 4 mg/ml of KCOH were compared by RNASeq to reveal gene modulations serving as markers for biological activity. The MIC and MBC values of KCOH were 8 and 16 mg/mL, respectively, against all tested S. enterica isolates. The MIC value was 4 mg/mL for both CRFa20 and CRFp85 sub-fractions, and a reduced MBC value was obtained for CRFp85 (4 mg/ml). Treatment of S. Enteritidis with KCOH revealed a concentration-dependent transcriptional signature. Compared to the control, 2 mg/ml of KCOH exposure resulted in 89 differentially expressed genes (DEGs), of which 53 and 36 were downregulated and upregulated, respectively. The upregulated genes included those involved in citrate metabolism, enterobactin synthesis and transport, and virulence. Exposure to 4 mg/ml KCOH led to the modulated expression of 376 genes, of which 233 were downregulated and 143 upregulated, which is 4.2 times more DEGs than from exposure to 2 mg/ml KCOH. The downregulated genes were related to flagellar motility, Salmonella Pathogenicity Island-1 (SPI-1), cell wall/membrane biogenesis, and transcription. Moreover, genes involved in energy production and conversion, carbohydrate transport and metabolism, and coenzyme transport and metabolism were upregulated during exposure to 4 mg/ml KCOH. Overall, 57 genes were differentially expressed (48 downregulated and 9 upregulated) in response to both concentrations. Both concentrations of KCOH downregulated expression of hilA, which is a major SPI-1 transcriptional regulator. This study provides information on the response of Salmonella exposed to cranberry extracts, which could be used in the control of this important foodborne pathogen.

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

Enteric fever is common in southeast Asia. However, there is little information on the circulating Salmonella enterica strains causing enteric fever in Myanmar. We performed antimicrobial susceptibility testing and whole genome sequencing on S. enterica bloodstream isolates from febrile patients aged ≥12 y attending two hospitals in Yangon, Myanmar, from 5 October 2015 through 4 October 2016. We identified the serovar of S. enterica, determined antimicrobial susceptibility and the molecular mechanisms of resistance. We analysed phylogenetic relationships among Myanmar S. enterica isolates and those with isolates from neighbouring countries. Of 73 S. enterica isolated, 39 (53%) were serovar Typhi and 34 (47%) were Paratyphi A. All isolates were susceptible to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole but resistant to ciprofloxacin. We identified mutations in chromosomal genes gyrA, gyrB and parC as responsible for fluoroquinolone resistance. All S. enterica Typhi isolates were of 4.3.1 subclade (formerly known as H58) and formed two closely related genotypic clusters; both clusters were most closely related to isolates from India from 2012. All S. enterica Paratyphi A were lineage C, clade C4 and were closely related. Our study describes currently circulating S. enterica serovars in Myanmar, the genetic basis of their antimicrobial resistance and provides a genotypic framework for epidemiologic study.

The diversity, evolution and ecology of Salmonella in venomous snakes.

BackgroundReptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles.Methodology/Principle findingsWe used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella, and found that a diverse range of serovars (n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae. Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S. diarizonae, S. enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo-inositol and allantoin.SignificanceWe present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella, including serovars which have been associated with disease in humans such as S. Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis.

Salmonella enterica persister cells form unstable small colony variants after in vitro exposure to ciprofloxacin

Persistence phenotype and small colony variants (SCVs) can be part of a bacterial bet-hedging strategy for survival under environmental stresses, such as antimicrobial exposure. These phenotypes are of particular concern in persistent and relapsing infections, since cells resume to normal growth after cessation of the stressful condition. In this context, we found persisters and unstable SCVs as phenotypic variants of Salmonella enterica that were able to survive ciprofloxacin exposure. A high heterogeneity in persister levels was observed among S. enterica isolates grown under planktonic and biofilm conditions and exposed to ciprofloxacin or ceftazidime, which may indicate persistence as a non-multidrug-tolerant phenotype. Nevertheless, a comparable variability was not found in the formation of SCVs among the isolates. Indeed, similar proportions of SCV in relation to normal colony phenotype (NCP) were maintained even after three successive cycles of ciprofloxacin exposure testing colonies from both origins (SCV or NCP). Additionally, we found filamentous and dividing cells in the same scanning electron microscopy images from both SCV and NCP. These findings lead us to hypothesize that besides variability among isolates, a single isolate may generate distinct populations of persisters, where cells growing under distinct conditions may adopt different and perhaps complementary survival strategies.

Antimicrobial resistance profiles and virulence genotyping of Salmonella enterica serovars recovered from broiler chickens and chicken carcasses in Egypt

BackgroundThis study aimed to survey the prevalence, antimicrobial resistance, and virulence-associated genes of Salmonella enterica recovered from broiler chickens and retail shops at El-Sharkia Province in Egypt. Salmonella virulence factors were determined using the polymerase chain reaction assays targeting the invA, csgD, hilC, bcfC, stn, avrA, mgtC, ompF, sopE1 and pefA genes.ResultsOne hundred tweenty out of 420- samples from broiler chickens’ cloacal swabs, farm environmental samples, and freshly dressed whole chicken carcasses were positive Salmonella species. The isolates were serotyped as S. Enteritidis as the most dominant serotypes. Interestingly, none of the isolates were resistant to imipenem. The multidrug resistance was determined in 76.7% of the isolates with multidrug antibiotic resistance index of 0.2–0.6. Eight virulence genes (invA, csgD, hilC, stn, bcfC, mgtC, avrA, and ompf) were characterized among 120 S. enterica isolates with variable frequencies, while sopE1and pefA genes that were completely absent in all isolates. Based on the combination of presence and absence of virulence genes, the most common genetic profile (P7, 30%) was invA and csgD genes.ConclusionS. Enteritidis and S. Typhimurium were the most common identified serotypes in the examined sources. Circulation of such strains in broiler farms required introducing special biosecurity and biocontrol measures for control of Salmonella. Such measures might limit the adverse effects of antibiotics and ensure the safety of the environment and animal-derived food.

CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR

BackgroundSalmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and requires expensive reagents. Here, we developed an R package CSESA (CRISPR-based Salmonella enterica Serotype Analyzer) to predict the serotype based on the CRISPR loci of S. enterica.ResultsCSESA has implemented the CRISPR typing method CLSPT and extended its coverage on diverse S. enterica serotypes. This package takes CRISPR sequences or the genome sequences as input and provides users with the predicted serotypes. CSESA has shown excellent performance with currently available sequences of S. enterica.ConclusionsCSESA is a convenient and useful tool for the prediction of S. enterica serotypes. The application of CSESA package can improve the efficiency of serotyping for S. enterica and reduce the burden of manpower resources. CSESA is freely available from CRAN at https://cran.r-project.org/web/packages/CSESA/.

Genetic Diversity of Salmonella enterica Strains Isolated from Sewage Samples of Different Hospitals in Bangladesh

The degree of salmonellosis is associated with the genetic diversity of the Salmonella enterica. Here, the genetic diversity of Salmonella enterica isolated from hospital sewage samples of Bangladesh were analyzed to elucidate the prevalence of S. enterica by random amplification of polymorphic DNA (RAPD) and amplified ribosomal DNA restriction analysis (ARDRA). Twenty six isolates were identified as S. enterica by cultural and biochemical methods as well as 16srDNA sequencing. These isolates showed two types of ARDRA and eight distinct RAPD patterns. All of these isolates possessed invA gene. However, agfA and fliC genes were found in 21 isolates and 16 isolates respectively. All of the isolates were resistant to rifamycin but most of them were sensitive to ceftriaxone and streptomycin. The study indicated that the genetic diversity is very high among the S. enterica isolates of Bangladesh. Therefore, such diversity may contribute to the future outbreak of salmonellosis in Bangladesh.
 Bangladesh J Microbiol, Volume 35 Number 1 June 2018, pp 57-60

Detection of virulence genes and investigation of the immunogenicity of outer membrane proteins of Salmonella enterica

A novel strategy for disarming quorum sensing in Pseudomonas aeruginosa-Chlorella emersonii KJ725233Sneha Sawant Desai, Reema Devi Singh, Sukhendu B Ghosh, Varsha Kelkar

Evaluation of temocillin for phenotypic carbapenemase screening of Escherichia coli and Salmonella enterica isolates in relation to the presence of genes encoding ESBLs and carbapenemase production.

The expression of enzymes of the OXA-48 carbapenemase group is difficult to detect by phenotypic methods owing to frequent low levels of carbapenem resistance and negative results with some screening methods. Temocillin has been shown to be a good option for phenotypic screening as it is hydrolysed by the OXA-48-group enzymes, whereas ESBLs, AmpC and some other carbapenemases have a lower hydrolytic effect on this antimicrobial. However, no epidemiological cut-off for temocillin is available. To evaluate temocillin MICs in relation to the presence or absence of genes encoding ESBLs and carbapenemases in Escherichia coli and Salmonella enterica. In this study, 111 E. coli and 102 S. enterica isolates, including WT and well-characterized ESBL-, AmpC- or carbapenemase-producing isolates, were tested by three independent laboratories. MICs were determined according to the CLSI guidelines by agar dilution with the test range from 0.5 to 512 mg/L temocillin and WGS was performed and analysed with ResFinder. Some overlap was detected between temocillin MICs for WT and ESBL- or AmpC-producing isolates. However, isolates carrying genes encoding carbapenemases showed a broader range of MICs for both E. coli and S. enterica. Higher MICs were observed for the OXA-48 group, VIM and some NDM-producing isolates, whereas isolates harbouring KPC enzymes showed low MICs. The results indicate that temocillin MICs enable phenotypic distinction between strains producing OXA-48-group enzymes and both WT susceptible and ESBL/AmpC-carrying isolates, whereas the distinction from other carbapenemases likely requires genotypic testing.

Occurrence, genetic diversity, and control of Salmonella enterica in native Brazilian farmed fish

Bacteria in the genus Salmonella are some of the most important foodborne pathogens worldwide. Despite their broad distribution, there are few records on these microorganisms in poikilothermic animals. Recently, Salmonella spp. were detected in the carcasses of native fish in Brazilian slaughterhouses, presenting the risk of foodborne-related salmonellosis. The aims of this study were to evaluate the occurrence, main serotypes, and genetic diversity of S. enterica in native farmed fish, as well as to determine appropriate control strategies. Five hundred and sixty-nine samples of rations, pond water, gill swabs, and feces of native fish were collected from commercial farms for bacteriological studies. The Salmonella isolates were identified using PCR and serotyped using a conventional method. Genetic diversity was evaluated by multi-locus sequence typing (MLST). Three orally administered products were tested to control Salmonella in experimentally infected fish: a probiotic; organic acids; and humic acid. Thirty-nine S. enterica isolates were obtained from water and fish samples. The isolates were classified as serotypes Brandenburg, Hadar, Heidelberg, Panama, and Saintpaul. One isolate could not be serotyped. Using MLST, the isolates were shown to represent 26 sequence types (STs), with 21 of these STs described here for the first time and five STs that were previously characterized. In the treatment trial, the groups of fish given feed with a probiotic and organic acids showed a 50% reduction in the number of fish positive for S. Hadar until the 20th day post-challenge. However, none of these products was able to clear S. Hadar from the guts of tambaqui. The strains of Salmonella enterica from fish showed high serotype and genetic diversity, which suggests multiple sources of infection and the absence of host-specific strains. The probiotic and organic acids might be used strategically prior to harvest to reduce Salmonella infection in fish herds, thereby decreasing the potential for carcass contamination.

Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

BackgroundSalmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states.ResultsWGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples.ConclusionsWGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars.

Molecular characterisation of antibiotic-resistant Salmonella enterica isolates recovered from meat in South Africa

Salmonella enterica is a leading cause of human gastroenteritis in both developed and developing countries, causing significant economic losses on humans and animals worldwide. There are several routes for contracting salmonellosis, but the consumption of contaminated foods is by far the most frequent cause of human infections. This study aimed to assess the prevalence and resistance determinants of S. enterica isolates obtained from meat. Swab samples from meat were cultured for the identification of Salmonella spp., and 239 presumptive S. enterica isolates were recovered, purified and kept in glycerol stocks. The S. enterica. confirmed by polymerase chain reaction (PCR) were further tested against 15 antimicrobials using the disc-diffusion method on Muller-Hinton agar and the genotypic antimicrobial resistance determinants by PCR. Resistance among tetracyclines, bêta-lactams, and 3rd generation cephalosporins was found to be most frequent with a noticeable rise in the number of multi-drug resistance ranging from two to seven antimicrobials. A total of 20 resistance determinants were assessed with their prevalence and distributions obtained as follows; [aminoglycosides: aadA (89%), aacC2 (100%), aphA1 (38%), aphA2 (0%) and strA (7%)], [β-lactams: (ampC 100%), blaTEM, (33%), blaZ (17%) and blaOXA (10%)], [Chloramphenicol: catI (9%), catII (7%), and cmIA1 (10%)] and [tetracyclines: tetA (57%), tetB (30%), tetC (11%), tetD (73%), tetK (20%) and tetM, (43%)], and [sulfonamides: sulI (82%), sulII (7%)]. The findings signify a high prevalence of multidrug-resistant (MDR) S. enterica isolates and resistance determinants indicating increased public health risks associated with the consumption of contaminated meat.

Characterization of Salmonella enterica serovars recovered from meat products legally and illegally imported into the EU reveals the presence of multiresistant and AmpC-producing isolates

BackgroundFood products of animal origin brought into the EU from third countries, both legally and illegally, can harbor foodborne pathogens such as Salmonella enterica. In this study, we examined five S. enterica isolates recovered either from legally imported chicken meat (n = 3) or from meat products confiscated from air travel passengers arriving in Germany (n = 2). The isolates were serotyped and further characterized by antimicrobial susceptibility testing, PCR-detection and sequencing of genes associated with antimicrobial resistances, and macrorestriction analysis. Transferability of resistance to third-generation cephalosporins was assessed by conjugation experiments and the plasmids tested for their incompatibility groups.ResultsThe three isolates from legal imports were identified as S. Heidelberg or as non-flagellated. All three isolates were identified as AmpC producers carrying blaCMY-2 and as non-susceptible to ciprofloxacin. They were additionally resistant to tetracycline and sulfamethoxazole. The blaCMY-2-carrying plasmids were transferable by conjugation and belonged to incompatibility groups IncI1 or IncA/C. The two isolates from illegally imported meat belonged to the serovars Infantis or Weltevreden. The former was phenotypically resistant to five classes of antimicrobial agents while the S. Weltevreden isolate was fully susceptible to all agents tested.ConclusionThe results of this study demonstrate that meat products imported from third countries, both legally and illegally, can harbor multiresistant Salmonella enterica. Consequently, these imports could constitute a source for the dissemination of antimicrobial resistant isolates, including those resistant to third-generation cephalosporins and fluoroquinolones.

Investigation of the Antimicrobial Susceptibility Profile, Virulence Genes, and Epidemiologic Relationship of Clinical Salmonella Isolates.

The objectives of this study were to investigate the epidemiologic relationship, prevalence of the beta-lactamase and virulence genes of clinical ampicillin-resistant Salmonella enterica. In vitro ampicillin susceptibilities of 117 Salmonella enterica isolates obtained between 2011-2012 from Ege University Hospital, Bacteriology Laboratory of Medical Microbiology Department were examined using disc diffusion assays in accordance with the CLSI guidelines. The MIC levels in the ampicillin-resistant bacteria were determined using the broth microdilution method. The resistant strains were serotyped by the Public Health Institution. Epidemiologic relations of resistant strains were evaluated using ERIC-PCR. The presence of beta-lactamase genes and virulence factors were detected using PCR. The 117 S. enterica strains had ten isolates that were resistant to ampicillin, and the MIC range of ampicillin was found as 512-128 μg/mL. Ampicillin-resistant strains were susceptible to nalidixic acid, ciprofloxacin, cefotaxime, sulfamethoxazole/trimethoprim. Four different serotypes were identified and isolates were grouped into seven clusters. Five isolates carried blaTEM , and two carried the blaCTX-M gene. However, it was determined that blaSHV and blaPER genes did not exist in these strains. Virulence genes invA, pipD, and sopB were found in all isolates. sifA, pefA, and sopE genes were found in seven, four, and three isolates, respectively. Our data suggest that the rate of ampicillin resistance in S. enterica isolates was 8.5% in the two year period, but this ratio was generally lower than rates abroad. blaCTX-M and blaTEM genes could be responsible for ampicillin resistance. The blaSHV gene, which is highly prevalent in our country, was not found in any strains. sopB and pipD genes, which might be associated with beta-lactam resistance, were found in all strains. It is also noteworthy that the three isolates containing the sopE gene, which is associated with epidemic cases, were of the same serotypes and epidemiologic clusters.

Discrimination of non-typhoid Salmonella serogroups and serotypes by Fourier Transform Infrared Spectroscopy: A comprehensive analysis

Simpler, quick and low-cost methods for routine Salmonella enterica typing are required for epidemiologic surveillance of this important zoonotic pathogen. In this study, using a comprehensive isolate collection, we investigated the potential of Fourier transform infrared spectroscopy (FTIRS) to discriminate the most clinically-relevant serogroups and serotypes of non-typhoid Salmonella. Moreover, the role of O-units composition on the FTIRS Salmonella discrimination was also explored.S. enterica isolates (n = 325; 2002–2015; different sources and countries), of 57 serotypes and 15 serogroups [including the most frequent ones, B-n = 122; C-n = 108; D-n = 43 and E-n = 33)] were analysed by FTIRS. Infrared spectra were analysed by Partial Least Square Discriminant Analysis (PLSDA) and/or Principal Component Analysis (PCA).The polysaccharides region provided the spectral sharpest differences being used in the subsequent Salmonella typing. Serogroups (B, C, D and E) discrimination was achieved with high accuracy (99.6% of correct assignments; PLSDA model). Differences in the O-unit structures composition of those serogroups are likely justifying the discrimination achieved. Other serogroups (G, H, K, L, M, N, O, T, U, Y, Z) were correctly predicted as not belonging to serogroups B, C, D nor E, except for 3 isolates of serogroups H (S. Sundsvall, n = 1) and K (S. Cerro, n = 2). In fact, O-unit structure of serogroup H and K shows some similarity with sub-serogroup C1 with the remaining serogroups presenting marked differences in this cellular component. The sub-serogroups discrimination was successfully achieved for C1, C2 and C3 (using PCA), and for E1-E2-E3 and E4 (by PLSDA). Appropriate serotype discrimination was obtained for most of S. Rissen from the remaining C1 serotypes (91.5%-PLSDA), and S. Enteritidis (D1) from the remaining D1/D2 serotypes (93.4%-PLSDA). The lack of available O-unit composition for particular serotypes prevents the elucidation of the role of this cellular component on the discrimination at serotype level obtained.FTIRS was able to discriminate relevant serogroups (B, C, D and E), sub-serogroups (C1, C2 and C3; E1-E2-E3 and E4) and particular important serotypes (S. Enteritidis, S. Rissen and S. Senftenberg). Further studies on O-antigen composition would clarify the fundaments of discrimination obtained by FTIRS.

Genetic characterisation of class 1 integrons among multidrug-resistant Salmonella serotypes in broiler chicken farms.

Antimicrobial resistance in Salmonella serotypes has been reported. Integrons play an important role in the dissemination of antimicrobial resistance genes in bacteria. Scarce literature is available on the identification of integrons in Salmonella isolated from broiler chickens. In this study, antimicrobial susceptibility testing and characterisation of class 1 integrons among multidrug-resistant (MDR) Salmonella enterica serotypes in broiler chicken farms in Egypt were performed. Antimicrobial susceptibility was determined by the disk diffusion method. PCR was performed to detect antimicrobial resistance genes and class 1 integrons in the tested Salmonella serotypes. Gene sequencing of the variable region of a class 1 integron was performed. Salmonella spp. were detected in 26 (13.5%) of 192 broiler samples, with Salmonella Enteritidis being the most frequently detected serotype, followed by Salmonella Kentucky and Salmonella Typhimurium and other serotypes. A very high resistance rate was observed to trimethoprim/sulfamethoxazole (100%), whilst a low resistance rate was observed to cefuroxime (57.7%). MDR S. enterica isolates displayed resistance to ciprofloxacin and azithromycin. Class 1 integrons were detected in 20 (76.9%) of the 26 Salmonella isolates. A high prevalence of class 1 integrons, as the first recorded percentage in the literature, associated with MDR Salmonella isolates was observed. Antimicrobial resistance rates in Salmonella serotypes from broiler chicken farms were alarming, especially for ciprofloxacin and azithromycin. Thus, another therapeutic strategy other than antimicrobials is recommended to prevent outbreaks of MDR Salmonella.

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals.

While antimicrobial resistance in Salmonella enterica is mainly attributed to large plasmids, small plasmids may also harbor antimicrobial resistance genes. Previously, three major groups of ColE1-like plasmids conferring kanamycin-resistance (KanR) in various S. enterica serotypes from diagnostic samples of human or animals were reported. In this study, over 200 KanR S. enterica isolates from slaughter samples, collected in 2010 and 2011 as a part of the animal arm of the National Antimicrobial Resistance Monitoring System, were screened for the presence of ColE1-like plasmids. Twenty-three KanR ColE1-like plasmids were successfully isolated. Restriction fragment mapping revealed five major plasmid groups with subgroups, including two new groups, X (n = 3) and Y/Y2/Y3 (n = 4), in addition to the previously identified groups A (n = 7), B (n = 6), and C/C3 (n = 3). Nearly 75% of the plasmid-carrying isolates were from turkey and included all the isolates carrying X and Y plasmids. All group X plasmids were from serotype Hadar. Serotype Senftenberg carried all the group Y plasmids and one group B plasmid. All Typhimurium isolates (n = 4) carried group A plasmids, while Newport isolates (n = 3) each carried a different plasmid group (A, B, or C). The presence of the selection bias in the NARMS strain collection prevents interpretation of findings at the population level. However, this study demonstrated that KanR ColE1-like plasmids are widely distributed among different S. enterica serotypes in the NARMS isolates and may play a role in dissemination of antimicrobial resistance genes.