Characterization of integrons and antimicrobial resistance genes in clinical isolates of Gram-negative bacteria from Palestinian hospitals

Sixty Gram-negative bacterial isolates were collected from Palestinian hospitals in 2006. Thirty-two (53.3%) isolates showed multidrug resistance phenotypes. PCR and DNA sequencing were used to characterize integrons and antimicrobial resistance genes. PCR screening showed that 19 (31.7%) and five (8.3%) isolates were positive for class 1 and class 2 integrons, respectively. DNA-sequencing results for the captured antimicrobial resistance gene cassettes within class 1 integrons identified the following genes: dihydrofolate reductases, dfrA1 , dfrA5 , dfrA7 , dfrA12, dfrA17 and dfrA25 ; aminoglycoside adenyltransferases, aadA1, aadA2 , aadA5, aadA12 and aadB ; aminoglycoside acetyltransferase, aac(6')-Ib ; and chloramphenicol resistance gene, cmlA1 . ESBL were identified in 25 (41.7%) isolates. The identified ESBL were bla _CTX-M-15, bla _CTX-M-56, bla _OXA-1, bla _SHV-1, bla _SHV-12, bla _SHV-32 and bla _TEM-1 genes. Moreover, we characterized the plasmid-mediated quinolone resistance genes, aac(6')-Ib-cr and qnrB2 , which were detected in seven (11.7%) and two (3.3%) isolates, respectively. In this study various types of antibiotic resistance genes have been identified in Gram-negative bacteria from Palestinian hospitals, many of which are reported in the Middle East area for the first time.     

Salmonella enterica isolates from pasture‐raised poultry exhibit antimicrobial resistance and class I integrons

Aims: While considerable foodborne pathogen research has been conducted on conventionally produced broilers and turkeys, few studies have focused on free‐range (organic) or pastured poultry. The current surveillance study was designed to isolate, identify and genetically characterize Salmonella from pastured poultry farm environment and from retail samples. Methods and Results: In this study, 59 isolates were collected from two pastured poultry farms (n = 164; pens, feed, water and insect traps) and retail carcasses (n = 36) from a local natural foods store and a local processing plant. All isolates were serotyped and analysed phenotypically (antimicrobial resistance profiles) and genotypically (DNA fingerprints, plasmid profiles and integron analysis). Salmonella enterica was detected using standard microbiological methods. Salmonella Kentucky was the most prevalent serotype detected from the sampled sources (53%), followed by Salmonella Enteritidis (24%), Bareilly (10%), Mbandaka (7%), Montevideo (5%) or Newport (2%). All isolates were resistant to sulfisoxazole and novobiocin, and the majority (40/59) possessed class I integrons shown by PCR detection. Each Salmonella serotype elicited a distinct pulsed‐field gel electrophoresis fingerprint profile, and unique differences were observed among the serotypes. Conclusions: The findings of this study show that Salmonella serotypes isolated from pasture‐raised poultry exhibit antimicrobial resistance and class I integrons. Significance and Impact of the Study: This study demonstrates that despite the cessation of antibiotic usage in poultry production, antibiotic resistant Salmonella may still be recovered from the environment and poultry products.     

Transfer of ampicillin resistance from Salmonella Typhimurium DT104 to Escherichia coli K12 in food

Aims: To investigate the transfer of antibiotic resistance from a donor Salmonella Typhimurium DT104 strain to a recipient Escherichia coli K12 strain. Methods and Results: Mating experiments were conducted in broth, milk and ground meat (beef) at incubation temperatures of 4, 15, 25 and 37°C for 18 and 36 h. Ampicillin‐resistance transfer was observed at similar frequencies in all transfer media at 25 and 37°C (10^?4 to 10^?5 log₁₀ CFU ml g^?1, transconjugants per recipient) for 18 h. At 15°C, transfer was observed in ground meat in the recipient strain (10^?6, log₁₀ CFU g^?1, transconjugants per recipient), but not in broth or milk. At 4°C, transfer did not occur in any of the examined mediums. Further analysis of the E. coli K12 nal^R transconjugant strain revealed the presence of a newly acquired plasmid (21 kbp) bearing the β‐lactamase gene bla_TEM. Transconjugants isolated on the basis of resistance to ampicillin did not acquire any other resistant markers. Conclusion: This study demonstrates the transfer of antibiotic resistance in food matrices at mid‐range temperatures. Significance and Impact of the Study: It highlights the involvement of food matrices in the dissemination of antibiotic‐resistant genes and the evolution of antibiotic‐resistant bacteria.     

Molecular characterization of antibiotic resistance in clinical Salmonella typhi isolated in Ghana

Fifty-eight clinical Salmonella typhi strains isolated from patients suspected of suffering from typhoid fever were obtained at the Korle-Bu Teaching Hospital and the Noguchi Memorial Institute for Medical Research, both located in Ghana, Africa. Each isolate was examined for susceptibility to ampicillin, chloramphenicol, streptomycin, tetracycline, and trimethoprim/sulfamethoxazole by the disk diffusion assay. Five of the isolates were resistant to all five antibiotics while 10 isolates were resistant to ampicillin, chloramphenicol, and trimethoprim/sulfamethoxazole, which are considered 'first line' antibiotics in the treatment of typhoid fever. Thirty-four isolates were resistant to at least one of the antibiotics tested and 62% of these isolates possessed conjugable plasmids belonging to incompatibility group IncHI. Ninety percent of the conjugable plasmids conferred a multiple drug-resistant phenotype on the strains harboring them. Additionally, 14 strains contained plasmids that were transformable and six of them encoded multiple drug resistance. Our findings indicate that multiple drug resistance to the 'first line' antibiotics in S. typhi may be more prevalent in Africa than previously thought.     

Identification and characterization of class 1 integron resistance gene cassettes among Salmonella strains isolated from healthy humans in China

Twenty-three strains of Salmonella spp. isolated from healthy humans in Guangdong, China, were examined for their susceptibility to ten common antibiotics and the presence of antibiotic resistance integrons. All the strains were resistant to at least one antibiotic, and 4 strains were positive for the intI1 gene. Polymerase chain reaction using in-F and in-B primers showed the existence of amplicons of 1,009 bp in two, 1,664 bp in one, and 1,009 bp and 1,664 bp in one of the intI1 -positive isolates, respectively. Sequence analysis revealed that the 1,009-bp amplicon harbored gene cassette aadA2, conferring resistance to spectinomycin, and the 1,664-bp amplicon harbored genes aadA5 and dfr17, conferring resistance to spectinomycin, streptomycin and trimethoprim. Meanwhile the experiments of plasmid conjugation and Southern hybridization with intI1 as the DNA probe indicated that all the integrons found in these strains were chromosomal. Because the strains carrying class 1 integrons were isolated from healthy humans, it suggests the need for all-round surveillance of the antibiotic resistance of pathogens.     

Incidence of Extended-Spectrum β-Lactamases and Characterization of Integrons in Extended-Spectrum β-Lactamase-producing Klebsiella pneumoniae Isolated in Shantou, China

This study is concerned with the level of antibiotic resistance of extended-spectrum β-lactamase （ESBL）-producing Klebsiella pneumoniae, isolated in Shantou, China, and its mechanism. Seventy- four non-repetitive clinical isolates of K. pneumoniae producing ESBLs were isolated over a period of 2 years. Antibiotic susceptibility, carried out by Epsilometer test, showed that most of the isolates were multiresistant. Polymerase chain reaction showed that, among the several types of β-lactamases, SHV was the most prevalent, TEM was the second most prevalent, and CTX-M was the least prevalent. Sixty-nine isolates were positive for integrase gene IntI1, but no IntI2 or IntI3 genes were found. The variable region of class 1 integrons were amplified and further identified by sequencing. Thirteen different gene cassettes and 11 different cassette combinations were detected. Dfr and aadA cassettes were predominant and cassette combinations dfrA12, orfF and aadA2 were most frequently found. No gene cassettes encoding ESBLs were found. Integrons were prevalent and played an important role in multidrug resistance in ESBL-producing K. pneumoniae.     

健康猪直肠粪便中沙门菌I类整合子与耐药基因的检测

目的了解安徽省规模化猪场健康猪直肠粪便中沙门菌分离株多重耐药情况及其与I类整合子和耐药基因的携带关系。方法采用标准K-B纸片法对22株沙门菌分离株进行15种抗生素敏感试验;应用PCR技术对沙门菌分离株进行I类整合子及耐药基因检测。结果 22株沙门菌分离株中有20株(90.91%)对2种以上抗生素耐药,属于多重耐药株,羧氨苄青霉素-四环素-卡那霉素-氯霉素-氟苯尼考是主要多重耐药谱;22株沙门菌中有19株(86.4%)携带I类整合子,tetB、aph(3)-IIa和cmlA基因分别检出最高。结论沙门菌多重耐药性与整合子携带之间的关系密切,耐药表型测定结果与耐药基因检测结果基本一致,基因组DNA携带的耐药基因种类多于质粒。     

Genetic analysis of multiple antimicrobial resistance in Salmonella isolated from diseased broilers in Egypt

To date, no information has been available on the molecular bases of antimicrobial resistance in Salmonella spp. from poultry in Egypt or even in Africa. Therefore, the objective of this study was to analyze, at the molecular level, the mechanisms of multidrug-resistance in isolates of Salmonella recovered from diseased broilers in Egypt. Twenty-one Salmonella isolates were identified; 13 of these isolates were Salmonella enterica serovar Enteritidis and eight Salmonella enterica serovar Typhimurium. 17 (81%). Salmonella isolates displayed multidrug resistance phenotypes, particularly against ampicillin, streptomycin, spectinomycin, kanamycin, tetracycline, chloramphenicol, and trimethoprim/sulfamethoxazole. PCR and DNA sequencing identified class 1 integrons in nine (42.9%) isolates and class 2 integrons in three (14.3%) isolates. The identified resistance genes within class 1 integrons were aminoglycoside adenyltransferase type A, aadA1, aadA2 and aadA5 and dihydrofolate reductase type A, dfrA1, dfrA5, dfrA12, dfrA15 and dfrA17. The β-lactamase encoding genes bla(TEM-1) and bla(CMY-2) and florfenicol resistance gene floR were also identified. Furthermore, the tetracycline resistance gene tet(A) was identified in 14 (66.7%) Salmonella isolates. To the best of our knowledge, this is the first report of the molecular basis of antimicrobial resistance in Salmonella spp. isolated from poultry in Africa.     

Molecular characterization of a carbapenem-hydrolyzing beta-lactamase from Chryseobacterium (Flavobacterium) indologenes

Chryseobacterium (Flavobacterium) indologenes 001 clinical strain was resistant to several beta-lactam classes including carbapenems. Shotgun cloning experiments of Sau3AI restricted genomic DNA of C. indologenes 001 into pBKCMV cloning vector followed by transformation into Escherichia coli DH10B gave one recombinant plasmid possessing a 4.2-kb DNA insert. It encoded a pI 7.2 beta-lactamase of 239 amino acids (IND-1) which is a metallo-enzyme with a broad spectrum beta-lactam hydrolysis profile. This class B carbapenem-hydrolyzing beta-lactamase shares the highest identity (43%) with BlaB from C. meningosepticum, thus showing heterogeneity of carbapenem-hydrolyzing beta-lactamases in Chryseobacterium spp.     

Molecular characterization of antimicrobial resistance in Gram-negative bacteria isolated from bovine mastitis in Egypt

The aim of this study was to characterize the genetic basis of multidrug resistance in Gram-negative bacteria isolated from bovine mastitis cases in Egypt. Multidrug resistance phenotypes were found in 34 of 112 (30.4%) Gram-negative bacterial isolates, which harbored at least one antimicrobial resistance gene. The most prevalent multidrug-resistant (MDR) species were Enterobacter cloacae (8 isolates, 7.1%), Klebsiella pneumoniae (7 isolates, 6.3%), Klebsiella oxytoca (7 isolates, 6.3%), Escherichia coli (5 isolates, 4.5%), and Citrobacter freundii (3 isolates, 2.7%). The most commonly observed resistance phenotypes were against ampicillin (97.0%), streptomycin (94.1%), tetracycline (91.2%), trimethoprim-sulfamethoxazole (88.2%), nalidixic acid (85.3%), and chloramphenicol (76.5%). Class 1 integrons were detected in 28 (25.0%) isolates. The gene cassettes within class 1 integrons included those encoding resistance to trimethoprim (dfrA1, dfrA5, dfrA7, dfrA12, dfrA15, dfrA17, and dfrA25), aminoglycosides (aadA1, aadA2, aadA5, aadA7, aadA12, aadA22, and aac(3)-Id), chloramphenicol (cmlA), erythromycin (ereA2), and rifampicin (arr-3). Class 2 integrons were identified in 6 isolates (5.4%) with three different profiles. Furthermore, the β-lactamase encoding genes, bla(TEM), bla(SHV), bla(CTX-M), and bla(OXA), the plasmid-mediated quinolone resistance genes, qnr and aac(6)-Ib-cr, and the florfenicol resistance gene, floR, were also identified. To the best of our knowledge, the results identified class 2 integrons, qnr and aac(6)-Ib-cr from cases of mastitis for the first time. This is the first report of molecular characterization for antimicrobial resistance in Gram-negative bacteria isolated from bovine mastitis in Africa.     

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.     

Contribution of multi-antimicrobial resistance to the population of antimicrobial resistant Escherichia coli isolated from apparently healthy pigs in Japan

The aim of this study was to clarify the involvement of tetracycline usage in resistance rates against other antimicrobials. Antimicrobial susceptibility testing was carried out on 545 porcine Escherichia coli isolates throughout Japan. As the result of analyzing by regions, resistance rates against kanamycin, oxytetracycline and trimethoprim in the Kanto/Koshinetu district were higher than those in some other districts. High resistance rates against kanamycin or trimethoprim in oxytetracycline-resistant isolates were also observed in the Kanto/Koshinetu district. The prevalence of multi-antimicrobial resistance through co-selection of resistances against kanamycin or trimethoprim by tetracycline usage could be the cause of regional differences in these resistances in porcine E. coli. By a communicative surveillance, kanamycin- and trimethoprim-resistance rates were likely to be elevated with tetracycline usage. Thus, usage of specific antimicrobial(s) is a remarkable viewpoint to control antimicrobial resistant bacteria.     

Prevalence and antimicrobial resistance in Salmonella enterica isolated from broiler chickens,pigs and meat products in Thailand–Cambodia border provinces

This study aimed to examine the prevalence and antimicrobial resistance (AMR) of Salmonella isolates from broiler chickens, pigs and their associated meat products in the Thailand–Cambodia border provinces. A total of 941 samples were collected from pigs and broiler chickens at slaughter houses and from carcasses at local fresh markets in Sa Kaeo, Thailand (n = 554) and Banteay Meanchey, Cambodia (n = 387) in 2014 and 2015. From these samples, 345 Salmonella isolates were collected from Sa Keao (n = 145; 23%) and Banteay Meanchey (n = 200; 47%) and assayed for antimicrobial susceptibility, class 1 integrons and extended‐spectrum β‐lactamase (ESBL) genes. Serovars Typhimurium (29%) and Rissen (29%) were the most common serotypes found in Thai and Cambodian isolates, respectively. Multidrug resistance was detected in 34% and 52% of isolates from Sa Keao and Banteay Meanchey, respectively. The majority of the Thai isolates were resistant to ampicillin (72.4%), whereas most Cambodian isolates were resistant to sulfamethoxazole (71%). Eleven isolates from Sa Keao and 44 from Banteay Meanchey carried class 1 integrons comprising resistance gene cassettes. The most common gene cassette array was dfrA12‐aadA2 (61.1%). Six isolates were ESBL producers. The β‐lactamase genes found included bla_TEM‐1, bla_CTX‐M‐55 and bla_CMY‐2. Some of these class 1 integrons and ESBL genes were located on conjugative plasmid. In conclusion, multidrug‐resistant Salmonella are common in pigs, chickens and their products in the Thailand–Cambodia border provinces. Our findings indicate that class 1 integrons play a role in spread of AMR in the strains in this study.     

鸡蛋生产链中沙门氏菌对抗生素及消毒剂的耐药性研究

为研究鸡蛋生产链中沙门氏菌的污染情况及抗生素、消毒剂耐药情况,本文鉴定了鸡蛋生产链中分离得到的111株沙门氏菌(Salmonella)血清型,并测定了抗生素和消毒剂对沙门氏菌的最小抑菌浓度(Minimum inhibitory concentrations, MICs),检测了其对抗生素和消毒剂的耐药基因的表达情况。研究结果表明,沙门氏菌对甲氧苄啶(Trimethoprim, TMP)耐药率最高(N=100,P=90.09%),对阿莫西林/克拉维酸(Amoxicillin and clavulanate, AMC)、头孢噻呋钠(Sodium ceftiofur, CFS)、庆大霉素(Gentamicin, CN)敏感。沙门氏菌共产生6种不同的耐药谱型,TMP是最主要的耐药谱型(N=36,P=32.43%),52.25%的菌株(N=58)具有多重耐药性。苯扎氯铵(Benzalkonium chloride, BC)与氯化十六烷基吡啶(Cetylpyridinium chloride, CPC)对沙门氏菌的MIC的范围分别为：8~128 μg/mL、8~256 μg/mL。相对于质控菌株Escherichia coli ATCC10536,101株沙门氏菌对BC和CPC同时具有较高的耐药性(P=90.99%),109株沙门氏菌对抗生素和消毒剂具有共同耐药性(P=98.20%)。抗生素耐药基因检出率最高为blaTEM(N=49, P=44.14%),未检测出qnrA、qnrB、qepA基因,仅检测出qacEΔ1消毒剂耐药基因(N=63, P=56.76%)。抗生素耐药基因sul1和消毒剂耐药基因qacEΔ1具有显著相关性(P<0.01)。S. Derby对TMP、土霉素(Oxytetracycline, OTC)、阿莫西林(Amoxicillin, AML)、环丙沙星(Ciprofloxacin, CIP)同时表现较高的耐药性,S. Derby检出了11种抗生素耐药基因,消毒剂耐药基因qacEΔ1的检出率为81.25%(N=52)。鸡场中养殖内环境沙门氏菌对抗生素和消毒剂的耐药率以及耐药基因检出率均高于养殖外环境,鸡蛋包装、储存及销售等环节中沙门氏菌耐药率及耐药基因检出率均较高。由此可见,鸡蛋生产链中沙门氏菌对抗生素、消毒剂耐药性较严重,且存在共同耐药的现象。因此,需要进一步规范防控鸡场中沙门氏菌,规范抗生素和消毒剂的使用以及加强鸡蛋生产链条中卫生安全的监管。     

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.