Microarray analysis of antimicrobial resistance genes in Salmonella enterica from preharvest poultry environment

Aims:  To detect antimicrobial resistance genes in Salmonella isolates from turkey flocks using the microarray technology.
Methods and Results:  A 775 gene probe oligonucleotide microarray was used to detect antimicrobial resistance genes in 34 isolates. All tetracycline-resistant Salmonella harboured tet(A) , tet(C) or tet(R) , with the exception of one Salmonella serotype Heidelberg isolate. The sul1 gene was detected in 11 of 16 sulfisoxazole-resistant isolates. The aadA , aadA1 , aadA2 , strA or strB genes were found in aminoglycoside-resistant isolates of Salm. Heidelberg, Salmonella serotype Senftenberg and untypeable Salmonella . The prevalence of mobile genetic elements, such as class I integron and transposon genes, in drug-resistant Salmonella isolates suggested that these elements may contribute to the dissemination of antimicrobial resistance genes in the preharvest poultry environment. Hierarchical clustering analysis demonstrated a close relationship between drug-resistant phenotypes and the corresponding antimicrobial resistance gene profiles.
Conclusions:  Salmonella serotypes isolated from the poultry environment carry multiple genes that can render them resistant to several antimicrobials used in poultry and humans.
Significance and Impact of the Study:  Multiple antimicrobial resistance genes in environmental Salmonella isolates could be identified efficiently by microarray analysis. Hierarchical clustering analysis of the data was also found to be a useful tool for analysing emerging patterns of drug resistance.     

Prevalence and antimicrobial susceptibility of Salmonella spp. isolates from US cattle in feedlots in 1999 and 2000

AIMS: Faecal samples from cattle in US feedlots were evaluated for the presence of Salmonella. When Salmonella isolates were recovered the antimicrobial resistance patterns were determined. METHODS AND RESULTS: Faecal samples were collected from pen floors in 73 feedlots in 12 states during the period from October 1999 to September 2000. Pens of cattle selected for sampling were those that had been in the feedlot for the shortest period of time, the longest period of time and a randomly selected pen from the remaining pens. Faecal samples were cultured for Salmonella spp. and all Salmonella isolates were categorized by serotype. The susceptibilities of all isolates were determined using a panel of 17 antimicrobials. Overall, 6.3% (654/10,417) of the samples cultured positive for Salmonella spp. and 22.2% (94/422) of pens and 50.7% (37/73) of feedlots had one or more positive samples. There was little difference in the proportion of positive samples from short-fed (6.1%, 212/3482), random (6.4%, 217/3400) and long-fed (6.4%, 224/3485) pens of cattle. One of two pens of cattle that could not be attributed to a pen type had a single positive sample (2.0%, 1/50). Samples collected during the period of April to June (6.8%, 209/3054) and July to September (11.4%, 286/2500) were more likely to be positive than those collected during October to December (4.0%, 73/1838) and January to March (2.8%, 86/3025). The most common serotypes of Salmonella were dissimilar from those that are typically seen in human illness and cattle illness. The majority of isolates (62.8%, 441/702) were sensitive to all of the antimicrobials tested. Resistance was most frequently observed to tetracycline (35.9%, 252/702) followed by streptomycin (11.1%, 78/702), ampicillin (10.4%, 73/702) and chloramphenicol (10.4%, 73/702). Multiple resistance (resistance to > or =2 antimicrobials) was observed for 11.7% (82/702) of the isolates. CONCLUSIONS: Salmonella was isolated at low frequency from faeces of feedlot cattle and the serotypes were not those commonly associated with human illness. In addition most of the Salmonella isolates were sensitive to all the antimicrobials tested. SIGNIFICANCE AND IMPACT OF THE STUDY: This study contributes to understanding the ecology of Salmonella in cattle feedlots and the prevalence of resistance among potential food-borne pathogens.     

Complete nucleotide sequence of a virulence plasmid of Salmonella enterica serovar Dublin and its phylogenetic relationship to the virulence plasmids of serovars Choleraesuis, Enteritidis and Typhimurium

The complete nucleotide sequence of pOU1113 (pSDVu), one of the two types of virulence plasmids of Salmonella enterica serovar Dublin, was determined. It contained 80 156 bp with 53.8 mol% G+C content. Approximately 70 genes could be discerned. Compared with pSTV, the virulence plasmid of serovar Typhimurium, pOU1113 was shorter owing to a missing region amounting to c. 10 kb; furthermore, except for a unique 10 849-bp region, the nucleotide as well as deduced amino acid sequences of pOU1113 were nearly identical to the corresponding regions of three S. enterica virulence plasmids, namely pSCV (virulence plasmid of Choleraesuis), pSTV and pSEV (virulence plasmids of Enteritidis), confirming their close phylogenetic relationship. Comparative analysis indicated that these virulence plasmids appeared to have descended by deletion from a relatively large plasmid to smaller ones, with some recombination events occurring over time. From a biological and evolutionary point of view, if the decreasing sizes of pOU1113 and pSCV truly reflect a process in which the virulence plasmid has been shedding unnecessary genes during evolution, our data suggest that some genes in the missing region, such as the pef and tra operons, could have a minimal role in maintaining the survival of the bacteria in their environmental niche.     

Characterization of antimicrobial resistance of Pseudomonas aeruginosa isolated from canine infections

Aims: To determine the prevalence of Pseudomonas aeruginosa among dogs with suspected soft tissue infections and to characterize these isolates. Methods and Results: Swabs were taken from infected soft tissues of 402 dogs. Pseudomonas aeruginosa strains were confirmed phenotypically and tested for susceptibility to 11 antimicrobial agents and genotyped by SpeI pulsed‐field gel electrophoresis (PFGE). The genetic basis of fluoroquinolone (FQ) resistance and the presence of integrons were also characterized. A total of 27 (6·7%) dogs tested positive for Ps. aeruginosa. Fourteen different SpeI patterns were observed in 25 typeable strains. Among the β‐lactams, three isolates presented resistance to ticarcillin and carbenicillin, while only one isolate exhibited resistance to ceftazidime. Among the aminoglycosides (AGs), three strains showed resistance to amikacin, and four strains exhibited resistance to gentamicin and tobramycin. Four strains with mutations that led to the substitution of Thr at position 83 with Ile in GyrA and the exchange of Ser at position 87 with Leu in ParC displayed resistance to all tested FQs. These strains also carried class 1 integrons and showed resistance to between 6 and 10 antimicrobials. These integrons included four different gene cassettes (aacA4‐aadA1, bla_OXA‐31‐aadA2, aadA1‐arr‐3‐catB3 and cmlA5‐cmlA‐aadA1). Conclusions: A small proportion of infected dogs treated in two animal hospitals in Beijing, China carried Ps. aeruginosa isolates. Low levels of resistance to anti‐pseudomonal agents were observed in these strains. Significance and Impact of the Study: This study is the first report on the antimicrobial resistance profiles of Ps. aeruginosa isolated from infected canine origin in China. Additionally, this is the first report of the oxacillin resistance gene bla_OXA‐31 in a canine Ps. aeruginosa isolate.     

The prevalence and antimicrobial resistance phenotypes of Salmonella,Escherichia coli and Enterococcus sp. in surface water

Surface water is prone to bacterial contamination as it receives wastes and pollutants from human and animal sources, and contaminated water may expose local populations to health risks. This review provides a brief overview on the prevalence and antimicrobial resistance (AR) phenotypes of Salmonella, Escherichia coli and Enterococcus, found in natural freshwaters. These bacteria are frequently detected in surface waters, sometimes as etiological agents of waterborne infections, and AR strains are not uncommonly identified in both developed and developing countries. Data relating to Salmonella, E. coli and Enterococcus present in environmental water are lacking, and in order to understand their development and dissemination using the One Health approach, understanding the prevalence, distribution and characteristics of the bacteria present in surface water as well as their potential sources is important. Furthermore, AR bacteria in natural watersheds are not well investigated and their impacts on human health and food safety are not well understood. As surface water is a receptacle for AR bacteria from human and animal sources and a vehicle for their dissemination, this is a crucial data gap in understanding AR and minimizing its spread. For this review, Salmonella, E. coli and Enterococcus were chosen to evaluate the presence of primary pathogens and opportunistic pathogens as well as to monitor AR trends in the environmental water. Studies around the world have demonstrated the widespread distribution of pathogenic and AR bacteria in surface waters of both developing and developed countries, confirming the importance of environmental waters as a reservoir for these bacteria and the need for more attention on the environmental bacteria for emerging AR.     

陕西食源性沙门氏菌耐药及相关基因

【目的】研究食源性沙门氏菌对常用抗生素的药敏性及相关耐药基因,更好的了解耐药性的产生和传播途径,确保食品安全。【方法】使用the Clinical and Laboratory Standards Institute推荐的琼脂稀释法测定沙门氏菌的药敏性,PCR和基因序列测定方法确定耐药沙门氏菌中整合子及其携带的耐药基因、与头孢菌素抗性相关的基因、沙门氏菌基因岛及与氟喹诺酮类抗生素耐药相关的基因突变。【结果】359株沙门氏菌中,67%的菌株对磺胺甲恶唑产生抗性,对甲氧苄啶/磺胺甲恶唑、四环素、卡那霉素、萘啶酮酸、氨苄西林、阿莫西林/克拉维酸、链霉素、氯霉素和庆大霉素、环丙沙星、头孢曲松、头孢西丁和头孢哌酮的耐药率分别为58%、56%、37%、35%、33%、32%、29%、26%、21%、16%、9%和8%。284株耐药菌中,79%的菌株可抗至少1种抗生素,25.9%可抗10种以上抗生素,2.5%可抗14种抗生素。耐药的Ⅰ类整合子以1.4kb最为常见,携带的耐药基因有aadA1、aadA2、aadA5、tetR、blaPSE-1、blaDHA-1、blaVEB-1、dhfrⅠ、dhfrⅤ、dhfrⅦ和dhfr17等。62株耐头孢曲松和/或头孢哌酮的沙门氏菌中,blaTEM和blaCMY-2基因的检出率分别为51.6%和56.5%。13.6%的沙门氏菌中检出了沙门氏菌基因岛。35株耐氟喹诺酮类抗生素的沙门氏菌的gyrA、parC和parE基因中共检出68个点突变,gyrA基因中常见突变为Ser83Phe、Ser83Tyr、Asp87Gly和Asp87Asn,parC基因中为Ser80Arg。parE基因中检出了Lys441Ile、Lys428Gln、Asp494Asn、Lys428Gln和Gly442Ser突变,这些点突变均为首次在食源性沙门氏菌中检出。【结论】陕西食源性沙门氏菌耐药状况严重,整合子、沙门氏菌基因岛和β-内酰胺酶编码基因的存在及解旋酶和拓扑异构酶基因突变是导致沙门氏菌耐药的重要机制。     

Species distribution,virulence factors and antimicrobial resistance of Acinetobacter spp. isolates from dogs and cats: a preliminary study

In this study, the prevalence of virulence factors and antimicrobial resistance among 67 Acinetobacter spp. isolates, consisting of 21 Acinetobacter baumannii and 46 non‐baumannii Acinetobacter obtained from companion animals, was investigated. PCR analysis showed that the most prevalent virulence gene was afa/draBC (29.9%), followed by papC (22.4%) and cvaC (20.9%). Antimicrobial susceptibility testing revealed that resistance to gentamicin (14.9%) and ciprofloxacin (11.9%) was relatively prevalent. Five gentamicin‐ and/or ciprofloxacin‐resistant A. baumannii strains were assigned to ST25, ST149, ST164, ST203 and ST1198. All ciprofloxacin‐resistant isolates harbored point mutations in gyrA and/or parC. To the best of our knowledge, this is the first report of preliminary monitoring of animal‐origin Acinetobacter spp. in Japan.

     

Epidemiological analysis of Salmonella enterica ssp. enterica serovars Hadar, Brancaster and Enteritidis from humans and broiler chickens in Senegal using pulsed-field gel electrophoresis and antibiotic susceptibility

AIMS: Salmonella Hadar, Salmonella Brancaster and Salmonella Enteritidis are the main Salmonella enterica ssp. enterica serovars isolated from poultry in Senegal. Our objective was to analyse the pulsed-field gel electrophoresis (PFGE) and antibioresistance patterns of strains belonging to these serovars and to assess the significance of broiler-chicken meat as a source of human infection. METHODS AND RESULTS: A total of 142 Salmonella isolates were analysed: 79 were isolated from Senegalese patients with sporadic diarrhoea (11 S. Hadar, nine S. Brancaster and 59 S. Enteritidis) and 63 from poultry (30 S. Hadar, 17 S. Brancaster and 16 S. Enteritidis). The PFGE of XbaI- and SpeI-digested chromosomal DNA gave 20 distinct profiles for S. Hadar, nine for S. Brancaster and 22 for S. Enteritidis. Each serovar was characterized by a major pulsotype which was X3S1 in 42% of S. Hadar, X8S1 in 53.8% of S. Brancaster and X1S2 in 43% of S. Enteritidis isolates. Human and poultry isolates of Salmonella had common PFGE patterns. Antibiosensitivity tests showed multiresistance (more than two drugs) was encountered in 14.5% of S. Hadar and in 5% of S. Enteritidis isolates. Resistance to quinolones was considered to be of particular importance and 14.5% of S. Hadar isolates were found to be resistant to nalidixic acid. CONLCUSIONS: The sharing of similar PFGE profiles among isolates from humans and poultry provided indirect evidence of Salmonella transmission from contaminated broiler meat. But most of the Salmonella isolates remained drug sensitive. SIGNIFICANCE AND IMPACT OF THE STUDY: Efforts are needed to eliminate Salmonella from poultry meat intended for human consumption. This study has also highlighted the importance of continuous surveillance to monitor antimicrobial resistance in bacteria associated with animals and humans.     

Phenotypic evidence for inducible multiple antimicrobial resistance in Salmonella choleraesuis

Multiple antimicrobial resistance (MAR) in Salmonella choleraesuis is becoming a major concern. It has been demonstrated that a MAR phenotype can be induced in Escherichia coli and other members of the Enterobacteriaceae by exposing the isolates to salicylates, various antimicrobials, or organic solvents used to combat and control bacterial infection. Therefore the purpose of the present study was to determine whether this marA-associated MAR-phenotype is inducible in S. choleraesuis. Isolates used in the present study were able to withstand toxic effects of the organic solvent cyclohexane naturally, or following exposure to the inducing compounds salicylate, tetracycline, or chloramphenicol. All isolates possessed fragments of marA with the predicted size of 408 bp when amplified using marA-specific primers by PCR. The resulting PCR products that were sequenced revealed that amplified S. choleraesuis marA was 99% and 85% homologous to the published Salmonella typhimurium and E. coli marA sequences respectively. Minimum inhibitory concentrations of tetracycline (P<0.08), chloramphenicol (P<0.001), rifampin (P<0.08), and nalidixic acid (P<0.001) against cyclohexane-tolerant mutants were significantly increased when compared with wild-type S. choleraesuis. Northern hybridization signals for both marA and acrB were increased in the induced isolates when compared to uninduced controls while soxS expression did not change between induced and uninduced cultures. The results suggest that marA is present in S. choleraesuis and a MAR-phenotype is inducible in S. choleraesuis presumably due to the overexpression of marA and acrB and not to the overexpression of soxS.     

食源性沙门氏菌耐药性检测及相关质粒

[目的]测定390株沙门氏菌的抗生素药敏性,研究部分多重耐药株中质粒与其宿主耐药表型之间的关系及其在接合过程中对耐药性水平转移的影响.[方法]使用选择性培养基分离到沙门氏菌并通过PCR确认后,按照琼脂稀释法测定分离株对供试抗生素的药敏性,试剂盒提取代表性多重耐药株中的质粒,HindⅢ酶切,DPS软件分析电泳后质粒图谱.通过接合试验研究质粒在抗生素抗性水平转移中的作用.[结果]沙门氏菌分离株对四环素耐药最为普遍(58.2%),其次为链霉素(42.8%)、卡那霉素(39%)和氨苄青霉素(38.2%),对头孢西丁、氯霉素、庆大霉素、头孢曲松、阿莫西林甲氧苄啶、头孢替呋钠和萘啶酮酸的耐药率分别为27.2%、26.9%、21%、19%、18.2%、17.9%、14.6%和12.3%.抗性质粒编码的相同或相似沙门氏菌耐药表型与其中所含的耐药质粒并不呈现出严格的对应关系.质粒携带的抗性基因可通过接合作用转移,接合效率在2.4×10-4到5.6×10-1之间.[结论]食源性沙门氏菌对常用抗生素的多重耐药已经成为普遍现象,抗性质粒的同源性与其宿主耐药表型无直接相关性,其携带的耐药基因可通过接合作用在不同细菌种属之间高频传递.     

鸡肉源沙门氏菌对喹诺酮和氟喹诺酮类抗生素耐药状况及相关基因

【目的】研究分离于陕西、河南、四川和北京四省(市)鸡肉源沙门氏菌对喹诺酮和部分氟喹诺酮类抗生素的药敏性及相关耐药基因,更好地了解耐药性的产生和传播途径,确保食品安全。【方法】用琼脂稀释法测定沙门氏菌的药敏性,用PCR和基因序列测定法确定耐药沙门氏菌中与(氟)喹诺酮类抗生素耐药相关的喹诺酮类抗性决定区基因突变及质粒携带的耐药基因。【结果】390株沙门氏菌中,63.59%的菌株对萘啶酮酸产生抗性,21.28%、16.67%和14.62%的菌株分别对环丙沙星、左氧氟沙星和加替沙星产生抗性。248株萘啶酮酸抗性菌中,aac(6’)-Ib-cr、qnrA、qnrB和qnrS基因的检出率分别为20.16%、10.89%、10.08%和1.61%。83株耐环丙沙星的菌株中,gyrA和parC基因的点突变共199个;其中gyrA基因中以Ser83Phe和Asp87Gly双突变最为常见,其次分别为Ser83Phe和Asp87Asn双突变、Ser83Tyr、Ser83Phe、Asp87Gly;parC基因的65个点突变均为Ser80Arg突变。【结论】四省市中鸡肉源沙门氏菌耐药状况严重,其解旋酶和拓扑异构酶基因突变及质粒携带的耐药基因是导致沙门氏菌耐药的重要机制。     

Effects of repeated cycles of acid challenge and growth on the phenotype and virulence of Salmonella enterica

Aims: The aim of the study was to investigate how stresses like low pH, which may be encountered in farms or food preparation premises, shape populations of Salmonella enterica by the selection of stress-resistant variants. Methods and Results: Stationary-phase cultures of S. enterica serovar Enteritidis and serovar Typhimurium (one strain of each) were exposed to pH 2·5 for up to 4 h, followed by growth at pH 7 for 48 h. This process was repeated 15 times in two separate experiments, which increased the acid resistance of the three out of four populations we obtained, by three- to fourfold. Sustainable variants derived from the populations showed changes in colony morphology, expression of SEF17 fimbriae, growth, increased heat resistance and reduced virulence. Conclusions: The study demonstrates that low pH environments can select for populations of S. enterica with persistent phenotypic changes such as increased acid resistance and occasionally increased SEF17 expression and lower virulence. Significance and Impact of the Study: There is a common belief that increased acid resistance coincides with increased virulence. This study demonstrates for the first time that increased acid resistance often impairs virulence and affects the general phenotype of S. enterica.     

Repeated therapeutic dosing selects macrolide‐resistant Campylobacter spp. in a turkey facility

Aims: This study assessed the effects of the therapeutic use of Tylan^® in a large‐scale turkey production facility on the selection of macrolide‐resistant Campylobacter. Methods and Results: A flock of production turkeys (c. 30 000 birds) was followed from brooding to slaughter, and the effects of macrolide application was assessed in one half of the flock from finishing stage to final product and compared against the control barn where no macrolide was used. Overall, Campylobacter prevalence in turkeys was almost 100% by 4 weeks of age. When Campylobacter prevalence was assessed in relation to treatment, high levels of macrolide resistance were evident in this group following treatment, with Campylobacter coli becoming the dominant strain type. Over time, and in the absence of a selection agent, the population of resistant strains decreased suggesting that there was a fitness cost associated with macrolide resistance carriage and persistence. Macrolide resistance was detected in the control barn at a very low level (four isolates recovered during the study), suggesting that the creation or selection of macrolide‐resistant Campylobacter was correlated with the treatment regime used. Molecular analysis of a selection of macrolide‐resistant Campylobacter recovered was assessed using PCR, RFLP and sequence analysis of the 23S rRNA. The majority of isolates displaying high‐level macrolide resistance (>256 μg ml^?1) possessed an A2075G transition mutation in the 23S rRNA and the CmeABC efflux pump. Conclusions: These studies suggest that macrolide resistance can be promoted through the application of treatment during the grow‐out phase and once established in a production facility has the potential to persist and be transferred to final product. Significance and Impact of the Study: The study highlights the prudent use of antimicrobials in treatment of disease in poultry. Of significance is the presence of macrolide‐resistant Campylobacter in poultry production and finished product as a consequence of macrolide usage.     

Prevalence, seasonal occurrence and antimicrobial resistance of Salmonella in poultry retail products in Greece

Aims: To detect the prevalence, the seasonal occurrence and distribution of Salmonella serotypes in poultry products and to determine the resistance profile of Salmonella isolates. Method and Results: A total of 96 skin-on chicken carcasses and 30 liver samples were analysed between May 2007 and May 2009 from twenty-two different commercial farm brands found in retail market countrywide. Salmonella was isolated from 38 (39·5%) of 96 chicken carcasses and from 10 (33·3%) of 30 liver samples. Higher isolation rate (60·4%) was observed in carcasses detected during summer (May to October), and lower isolation rate (18·7%) was observed in carcasses detected during winter (November to April); in liver samples, the positive rates were 53·4 and 13·2%, respectively. Twelve serotypes were detected with the serotypes Hadar, Enteritidis and Blockley being the most prevalent at 29·2, 22·9 and 12·5%, respectively. Nine of 11 Salm. Enteritidis isolates occurred during summer. Of 48 isolates, 38 (79%) were resistant to one or more of the antimicrobial agents used. The highest resistance rates were found to the following antimicrobials: streptomycin (64·5%), tetracycline (56·2%), nalidixic acid (39·5%), ampicillin and rifampicin (33·3%). Conclusions: The relatively high Salmonella spp. contamination rates of raw chicken meat and liver have been detected. Salm. Enteritidis isolates peaked in summer, increasing the risk to human health. Antibiotic resistance of Salmonella still remains a threat as resistance plasmids may be extensively shared between animal and humans. Significance and Impact of the Study: The study enabled us to improve the data on the seasonal occurrence of Salmonella and to determine the antimicrobial pattern profile and trends in Salmonella strains isolated from poultry retail products in Greece.     

Transmission of Salmonella enterica serotype Typhimurium in poultry with and without antimicrobial selective pressure

AIMS: To determine the effect of antimicrobial selective pressure on the transmission of antimicrobial resistant and sensitive strains of Salmonella in poultry. METHODS AND RESULTS: Eight pens housed 12 broiler chicks each. Two chicks in four of the pens were inoculated with a Salm. Typhimurium strain resistant to 12 antimicrobials (including tetracycline), and two chicks in each of the four other pens were inoculated with a strain sensitive to all antimicrobials tested. Two pens inoculated with each strain were treated with chlortetracycline and two were not. Chicks were killed on day 7 and caeca were cultured for Salmonella. Experiments were performed independently twice. Chicks exposed to pen mates inoculated with the resistant strain and treated with tetracycline were 90% positive for Salmonella; whereas 60% of chicks given no antimicrobials were positive. Chicks exposed to the sensitive strain were 95% positive with tetracycline treatment and 90% positive without treatment. CONCLUSIONS: A multidrug-resistant Salm. Typhimurium strain had significantly increased transmission when chicks were treated with tetracycline. Transmission of a sensitive strain was not inhibited by antimicrobial selective pressure at recommended therapeutic dose. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates that antimicrobial usage may influence the transmission of antimicrobial-resistant pathogens in poultry.