Class 1 integrons and resistance gene cassettes among multidrug resistant Salmonella serovars isolated from slaughter animals and foods of animal origin in Ethiopia

In Silico Detection of Antimicrobial Resistance Integrons in Salmonella enterica Isolates from Countries of the Andean Community

Antimicrobial resistance genes are often associated with integrons, which promote their movement between and within DNA molecules. IntFinder 1.0 and I-VIP v1.2 were used for the detection of integrons and their associated resistance genes in assembled sequences and raw reads. A dataset comprising 1688 sequenced Salmonella enterica isolates from countries of the Andean Community was developed. A total of 749 and 680 integrons were identified by IntFinder 1.0 and I-VIP v1.2, respectively; class 2 integrons were the most abundant followed by class 1, whereas no class 3 integrons were detected. These elements were mainly associated with isolates from animal sources. S. Infantis ST32 contained the majority of integrons. Trimethoprim resistance genes (dfrA) were found in greater numbers than others, including aadA and bla genes. The presence of these resistance integrons may come as a response to antibiotic misuse, especially of co-trimoxazole. This represents a public health risk as novel resistant strains might appear due to gene dissemination. The information gathered from in silico studies not only contributes to our understanding of integron dynamics in pathogenic Salmonella, but also helps identify potential emergent patterns of resistance in the region, which is fundamental for developing pertinent antibiotic surveillance programs.

Prevalence of IncFIB Plasmids Found among Salmonella enterica Serovar Schwarzengrund Isolates from Animal Sources in Taiwan Using Whole-Genome Sequencing

Salmonella enterica serovar Schwarzengrund is one of the most frequently isolated Salmonella serotypes responsible for human and poultry infections in Taiwan, and it has raised public health concerns. To better facilitate the understanding of transmission patterns and the dynamics of epidemics, sharing molecular data on pathogen profiles is urgently needed. The objectives of the current study were to determine and establish baseline data of S. enterica serovar Schwarzengrund isolates from 23 epidemiologically unrelated sources from year 2000 to 2018 and examine their phenotypic and genotypic characteristics. Genomic DNA of the Salmonella isolates was extracted and subjected to whole-genome sequencing using an Illumina platform. Results showed that all selected isolates exhibited multidrug resistance, and six of those were resistant to ciprofloxacin phenotypically. Genotypically, these isolates carried genes resistant to aminoglycoside (100%), phenicol (91.3%), β-lactams (69.5%), folate pathway antagonist (100%), tetracycline (82.6%), and fluoroquinolone (4.3%). Moreover, these isolates harbor integrons with five different gene cassettes identified for the first time, which are associated with resistance to trimethoprim, streptomycin, tetracycline, sulfonamide, chloramphenicol, and gentamicin. Furthermore, prevalence of IncFIB plasmid was found among studied isolates, which may increase its ability to colonize the chicken cecum and cause extra-intestinal disease. Salmonella pathogenicity islands SPI-1 to SPI-5, SPI-13, and SPI-14, as well as C63PI locus, were also detected in all isolates. This study demonstrated that a considerable high antimicrobial resistance with high virulence levels of Salmonella were found from animal sources. Sharing data on these pathogen profiles can not only help increase the reproducibility and accessibility of genomic analysis but can also support surveillance and epidemiological investigations for salmonellosis in the region.

An insight into the exploration of proliferation of antibiotic resistance genes in high-fat diet induced obesity mice

Using mice as an animal model, we first demonstrated the significant proliferation of ARGs and the change of mobile genetic elements (MGEs) in high-fat diet induced obesity (DIO) mice, which the ermB and tnpA-03 genes mostly increased, illuminating that DIO could enrich the abundance of ARGs. Additionally, Lactobacillus sharply increased in the DIO mice and might contribute to the proliferation of ARGs and dramatical change of MGEs in the HFD groups. Finally, procrustes analysis showed the explanatory variables of the MGEs, the metabolites, and the microbial communities for the ARGs accounted for 94.3%, 53.4%, and 68.1%, respectively, and implying that MGEs might be the most direct factor affecting ARGs, and microbiota could be the main driver of the proliferation of ARGs in the DIO mice.

Phenotypic and genotypic characterization of temporally related nontyphoidal Salmonella strains isolated from humans and food animals in central Ethiopia

Salmonella is one of the common causes of food-borne bacterial illnesses. The primary sources of human nontyphoidal Salmonella (NTS) infection are food animals. This study characterized temporally and spatially related Salmonella isolated during April 2013 to March 2014 from faeces of diarrhoeic human patients in Addis Ababa (n = 68) and food animals (n = 84) in Addis Ababa and surrounding districts (dairy cattle, n = 30; slaughtered cattle, n = 20; poultry, n = 26; swine n = 8). Isolates were serotyped, page typed and tested for antimicrobial susceptibility using Kirby-Bauer disc diffusion method, and genotyped by pulsed-field gel electrophoresis (PFGE). The dominant Salmonella serovars isolated from food animals were S. Saintpaul (38.1%), S. Typhimurium (17.9%) and S. Kentucky (9.5%), whereas in humans, S. Typhimurium (39.7%), S. Virchow (30.9%) and S. Kottbus (10.3%) were frequently isolated. Resistance to streptomycin, sulfisoxazole, tetracycline, ampicillin and cephalothin was higher in animal isolates than human isolates, and mean number of antimicrobials to which isolates were resistant was significantly higher in isolates from cattle and poultry compared to those from humans (p < 0.05). All S. Kentucky isolated from animals and humans were multidrug resistant (MDR) with shared resistance phenotype (AmpCfCipTeSuSNa). Although this study involved small sample size and was not able to show clear epidemiological linkage among isolates from various sources, genotyping by PFGE analysis demonstrated circulation of closely related genotypes of S. Virchow, S. Typhimurium and S. Kentucky among humans and food animals. Detection of related Salmonella isolates from humans and animals, the high MDR status of isolates from animals and close proximity of farms and human residential areas in the absence of appropriate biosecurity present major public health problem. Integrated surveillance of Salmonella serovars in humans and animals and implementation of appropriate hazard analysis and pathogen control strategies along critical points of the food chain from farm to table is recommended.

Effects of chlortetracycline and copper on tetracyclines and copper resistance genes and microbial community during swine manure anaerobic digestion

As antibiotic and heavy metals are over used in the livestock industry, animal manure is a reservoir of antibiotic resistance genes (ARGs). Anaerobic digestion has been reported to have the potential to reduce ARGs. However, few studies investigated whether reduction of ARGs would be affected by different external pressures including antibiotics and heavy metals during anaerobic digestion. The purpose of this study was thus to investigate effects of both chlortetracycline (CTC) and Cu on reduction of ARGs, heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) during the swine manure anaerobic digestion. The results showed that the predominant ARGs (tetO, tetW, tetX, tetL) could be effectively reduced (approximately 1.00 log copies/g TS) through mesophilic anaerobic digestion. Microbial community evolution was the main driver. It was interesting that Treponema might indicate the termination of anaerobic digestion and compete with ARGs host bacteria. Addition of CTC, Cu and CTC+Cu affected microbial community change and hindered removal of ARGs, especially, CTC+Cu seriously affected Treponema and ARGs during anaerobic digestion.

Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs

Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles indexed in the Medline and AJOL literature databases was conducted. We report on the findings of 43 eligible studies documenting local or pandemic fluoroquinolone-resistant enteric clones in sub-Sahara African countries. Most reports are of invasive non-typhoidal Salmonella and Escherichia coli lineages and there have been three reports of cholera outbreaks caused by fluoroquinolone-resistant Vibrio cholerae O1. Fluoroquinolone-resistant clones have also been reported from commensals and animal isolates but there are few data for non-Enterobacteriaceae and almost none for difficult-to-culture Campylobacter spp. Fluoroquinolone-resistant lineages identified in African countries were universally resistant to multiple other classes of antibacterial agents. Although as many as 972 non-duplicate articles refer to fluoroquinolone resistance in enteric bacteria from Africa, most do not report on subtypes and therefore information on the epidemiology of fluoroquinolone-resistant clones is available from only a handful of countries in the subcontinent. When resistance is reported, resistance mechanisms and lineage information is rarely investigated. Insufficient attention has been given to molecular and sequence-based methods necessary for identifying and tracking resistant clones in Africa and more research is needed in this area.

Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy-upland rotation system

This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy-upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of five tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), two sulfonamide ARGs (sul1 and sul2) and one genetic element (IntI1) was quantified. NPK application showed only slight or no impact on soil ARGs abundances compared with the control without fertilizer. Soil ARGs abundances could be increased by manure-NPK application but was related to manure dosage (2250-9000 kg ha(-1)). Principal component analysis (PCA) showed that the soil ARG profile of the treatment with 9000 kg ha(-1) manure separated clearly from the other treatments; the ARGs that contributed most to the discrimination of this treatment were tetA, tetG, tetW, sul1, sul2 and IntI1. Community level physiological profile (CLPP) analysis showed that increasing manure dosage from 4500 kg ha(-1) to 9000 kg ha(-1) induced a sharp increase in almost all of the detected ARGs but would not change the microbial community at large. However, 9000 kg ha(-1) manure application produced a decline in soil microbial activity. Determination of antibiotics and heavy metals in soils suggested that the observed bloom of soil ARGs might associate closely with the accumulation of copper and zinc in soil.

Resistance-Gene Cassettes Associated With Salmonella enterica Genotypes

BACKGROUND

The epidemiology of salmonellosis is complex because of the diversity and different serotypes of Salmonella enterica (S. enterica) that occur in different reservoirs and geographic incidences.

OBJECTIVES

To determine the genotype distribution and resistance-gene content of 2 classes of integron among S. enterica isolates.

METHODS

Thirty-six S. enterica species were isolated and tested for their serological distribution and the resistance-gene contents of 2 classes of integron, as well as for their genetic diversity, using the pulsed-field gel electrophoresis (PFGE) genotyping method.

RESULTS

Serogroups E (36.1%) and D (30.5%) were dominant among the isolates. All of the isolates in serogroup D belonged to the serovar enteritidis. The aadA1 gene was found within all resistance-gene cassettes. We observed 4 common and 26 single pulsotypes among the isolates, which indicated a high degree of genetic diversity among the isolates. Using the PulseNet International standard protocol, it was found that these isolates were different from those reported previously in Iran.

CONCLUSIONS

The presence of a few common and new pulsotypes among the isolates suggests the emergence and spread of new clones of S. enterica in Iran.

A meta-analysis of the proportion of animal Salmonella isolates resistant to drugs used against human salmonellosis in Ethiopia

Background

The emergence and spread of drug resistant Salmonellae of both human and animal origins are global concerns and worrisome in countries where the risk of infection is high and treatment options are limited. The objective of this study was to estimate the proportions of animal isolates resistant to antimicrobials used against human salmonellosis in Ethiopia.

Methods

Published studies on the antimicrobial resistance features of Salmonellae isolated from food animals of Ethiopia were searched in Medline, Google Scholar and the lists of references of articles. Eligible studies were selected by using inclusion and exclusion criteria and data were extracted. The extracted data included the host species, the numbers of isolates and the numbers of ampicillin, co-trimoxazole, chloramphenicol, ceftriaxone and ciprofloxacin resistant isolates. The risks of bias were assessed and the percentages of the variations of the estimates attributable to heterogeneities were quantified. Pooled proportions were estimated by the DerSimonian and Laird random effects model.

Results

Five hundred and fifty four Salmonellae isolated from cattle, camels, sheep, goats and pigs were tested with a variety of antimicrobials. The percentages of the variations attributable to heterogeneities were low for chloramphenicol and ceftriaxone (I² = 0) and high for ampicillin, co-trimoxazole and ciprofloxacin resistance estimates (I² > 75%). The pooled estimate of ampicillin resistant isolates was higher in slaughtered ruminants (17.28%) than in pigs (3.95%), (p < 0.001). The pooled estimates of co-trimoxazole resistant isolates in true ruminants (4.35%) and pigs (1.12%) were not significantly different (p > 0.05). The overall pooled estimates of chloramphenicol and ceftriaxone resistant isolates were 2.24% and 1.25%, respectively. Seven serotypes have been reported to be resistant to antimicrobials uncommonly used in veterinary clinical practice in Ethiopia.

Conclusions

Among Salmonellae of farm animals, there exist strains that are resistant to drugs used in the therapeutic management of human salmonellosis in Ethiopia. Intervention measures should be taken to ensure the prudent use of antimicrobials and curb the spread of high risk strains across the country.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-015-0835-x) contains supplementary material, which is available to authorized users.

A meta-analysis of the proportion of antimicrobial resistant human Salmonella isolates in Ethiopia

BACKGROUND

Antimicrobial resistant Salmonella is a global problem and recently, a strain on the verge of pan-resistance was reported. In Ethiopia, the therapeutic management of Salmonellosis is difficult because drug sensitivity tests are not routinely carried out and treatment alternatives are not available in most health care facilities. The objectives of this study were to estimate the temporal changes and proportions of drug resistant isolates in Ethiopia.

METHODS

Published studies on drug resistant Salmonella isolates were searched in Medline, Google Scholar and the lists of references of articles. Eligible studies were selected by using inclusion and exclusion criteria. Generic, methodological and statistical information were extracted from the eligible studies. The extracted data included the proportions of ampicillin, co-trimoxazole, chloramphenicol, ceftriaxone, ciprofloxacin and multi-drug resistant isolates. Pooled proportions were estimated by a random effects model.

RESULTS

The odds of multi-drug resistant isolates in the 2000s was higher than before the 1990s (OR =18.86, 95% CI = 13.08, 27.19). The pooled proportions of ampicillin, co-trimoxazole, chloramphenicol, ciprofloxacin and multi-drug resistant isolates in the 2000s were 86.01%, 68.01%, 62.08%, 3.61% and 79.56% respectively. S. Concord (>97%) was resistant to ampicillin, co-trimoxazole, chloramphenicol and ceftriaxone.

CONCLUSION

The proportion of drug resistant isolates has increased since the 1970s. All drugs currently used for the treatment of Salmonellosis but ciprofloxacin are not reliable for an empirical therapy. Alternative drugs should be included in the essential drug list and measures should be taken to re-enforce the drug use policy.

Characterization of multidrug-resistant Salmonella enterica serovars Indiana and Enteritidis from chickens in Eastern China

A total of 310 Salmonella isolates were isolated from 6 broiler farms in Eastern China, serotyped according to the Kauffmann-White classification. All isolates were examined for susceptibility to 17 commonly used antimicrobial agents, representative isolates were examined for resistance genes and class I integrons using PCR technology. Clonality was determined by pulsed-field gel electrophoresis (PFGE). There were two serotypes detected in the 310 Salmonella strains, which included 133 Salmonella enterica serovar Indiana isolates and 177 Salmonella enterica serovar Enteritidis isolates. Antimicrobial sensitivity results showed that the isolates were generally resistant to sulfamethoxazole, ampicillin, tetracycline, doxycycline and trimethoprim, and 95% of the isolates sensitive to amikacin and polymyxin. Among all Salmonella enterica serovar Indiana isolates, 108 (81.2%) possessed the blaTEM, floR, tetA, strA and aac (6')-Ib-cr resistance genes. The detected carriage rate of class 1 integrons was 66.5% (206/310), with 6 strains carrying gene integron cassette dfr17-aadA5. The increasing frequency of multidrug resistance rate in Salmonella was associated with increasing prevalence of int1 genes (rs = 0.938, P = 0.00039). The int1, blaTEM, floR, tetA, strA and aac (6')-Ib-cr positive Salmonella enterica serovar Indiana isolates showed five major patterns as determined by PFGE. Most isolates exhibited the common PFGE patterns found from the chicken farms, suggesting that many multidrug-resistant isolates of Salmonella enterica serovar Indiana prevailed in these sources. Some isolates with similar antimicrobial resistance patterns represented a variety of Salmonella enterica serovar Indiana genotypes, and were derived from a different clone.

Investigation of Class I Integron in Salmonella infantis and Its Association With Drug Resistance

Background:

Infection with non-typhoid Salmonella (NTS) is one of the most important health problems all over the world. Antimicrobial drug resistance is increasing among Salmonella infantis species.

Objectives:

The aim of this study was to investigate the frequency of presence of class 1 integrons in S. infantis species as well as its association with drug resistance.

Materials and Methods:

This cross-sectional study was performed on 50 S. infantis isolated strains, collected from chicken samples between 2009-2011. These strains were identified by standard biochemical tests and serology. Antibiotic susceptibility profiles and minimum inhibitory concentration determination for 14 antibacterial agents were performed using micro dilution and disk diffusion methods. The detection of class 1 integron was performed by the PCR method. The demographic and microbiological data for the integron positive and negative isolates were compared by SPSS software.

Results:

Eighteen out of 50 (36%) of isolated S. infantis species had intl gene. The isolated bacteria were sensitive to cefotaxime and ciprofloxacin (100%). Also isolates were resistant to nalidixic acid, tetracycline and streptomycin. All isolate with class 1 integron were multidrug resistant.

Conclusions:

The result of this study showed that due to increased level of drug resistance in S. infantis and the presence of class 1 integron in these strains, resistance can be transferred to other food borne pathogens.

Multiplex TaqMan® detection of pathogenic and multi-drug resistant Salmonella

Overuse of antibiotics in the medical and animal industries is one of the major causes for the development of multi-drug-resistant (MDR) food pathogens that are often difficult to treat. In the past few years, higher incidences of outbreaks caused by MDR Salmonella have been increasingly documented. The objective of this study was to develop a rapid multiplex real-time polymerase chain reaction (PCR) assay for simultaneous detection of pathogenic and MDR Salmonella spp. A multiplex TaqMan®real-time PCR was designed by targeting the invasin virulence gene (invA), and four commonly found antibiotic resistance genes, viz. ampicillin, chloramphenicol, streptomycin and tetracycline. To avoid false negative results and to increase the reliability of the assay, an internal amplification control (IAC) was added which was detected using a locked nucleic acid (LNA) probe. In serially diluted (5 ng-50 fg) DNA samples, the assay was able to detect 100 genomic equivalents of Salmonella, while in a multiplex format, the sensitivity was 1000 genomic equivalents. The assay performed equally well on artificially contaminated samples of beef trim, ground beef of different fat contents (73:27, 80:20, 85:15 and 93:7), chicken rinse, ground chicken, ground turkey, egg, spinach and tomato. While the detection limit for un-enriched inoculated food samples was 10(4) CFU/g, this was improved to 10 CFU/g after a 12-h enrichment in buffered peptone water, with 100% reproducibility. The multiplex real-time assay developed in this study can be used as a valuable tool to detect MDR virulent Salmonella, thus enhancing the safety of food.

Phenotypic and genotypic characterization of Salmonella enterica recovered from poultry meat in Tunisia and identification of new genetic traits

Thirty-seven Salmonella enterica isolates obtained from poultry meat in Tunisia were included in this study for characterization of antibiotic resistance mechanisms. High percentages of resistance were detected to ampicillin, sulfonamides, tetracycline, nalidixic acid, and streptomycin (32.4%-89.2%), and lower percentages to amoxicillin-clavulanic acid, kanamycin, amikacin, trimethoprim-sulfamethoxazol, and chloramphenicol (2.7%-18.9%). All strains showed susceptibility to ceftazidime, cefotaxime, gentamicin, and ciprofloxacin. Class 1 integrons were detected in 30% of Salmonella isolates, and four different gene cassette arrangements were detected, including genes implicated in resistance to aminoglycosides (aadA1 and aadA2) and trimethoprim (dfrA1). Four different Pc variants (PcW, PcH1, PcH1(TTN-10), PcW(TGN-10)) with inactive P2 have been found among these isolates. Integron-positive isolates were ascribed to eight different serotypes. A Salmonella Schwarzengrund isolate harbored a new class 1 integron containing the qacH-dfrA1b-aadA1b-catB2 gene cassette arrangement, with the very unusual PcH1(TTN-10) promoter, which has been registered in GenBank (accession no. HQ874651). Different plasmid replicon types were demonstrated among integron-positive isolates: IncI1 (8 isolates), IncN (8), IncP (2), IncFIB (2), and IncFII (2). Ten different pulsed-field gel electrophoresis profiles were detected among the 11 integron-positive isolates and 8 different sequence types were identified by multilocus sequence typing, one of them (registered as ST867) was new, detected in 3 Salmonella Zanzibar isolates. A high diversity of clones is observed among poultry Salmonella isolates and a high proportion of them show a multiresistant phenotype with very diverse mobile genetic structures that could be implicated in bacterial dissemination in different environments.

Salmonella genomic islands and antibiotic resistance in Salmonella enterica

Antibiotic resistance in several Salmonella enterica serovars that cause gastrointestinal disease in humans is due to a set of related genomic islands carrying a class 1 integron, which carries the resistance genes. Salmonella genomic island 1 (SGI1), the first island of this type, was found in S. enterica serovar Typhimurium DT104 isolates, which are resistant to ampicillin, chloramphenicol, florfenicol, streptomycin, spectinomycin, sulfonamides and tetracycline. Several Salmonella serovars and Proteus mirablis have since been shown to harbor SGI1 or related islands carrying various sets of resistance genes and some distinct groups have emerged. SGI1 is an integrative mobilizable element and can be transferred experimentally into Escherichia coli. However, within serovars, isolates recovered from different parts of the world appear to be clonal, indicating that SGI1 movement may be rare. Potential reservoirs in food-producing animals or in ornamental fish have been identified for some serovars.

A predominant multidrug-resistant Salmonella enterica serovar Saintpaul clonal line in German turkey and related food products

Recently, Salmonella enterica subsp. enterica serovar Saintpaul has increasingly been observed in several countries, including Germany. However, the pathogenic potential and epidemiology of this serovar are not very well known. This study describes biological attributes of S. Saintpaul isolates obtained from turkeys in Germany based on characterization of their pheno- and genotypic properties. Fifty-five S. Saintpaul isolates from German turkeys and turkey-derived food products isolated from 2000 to 2007 were analyzed by using antimicrobial agent, organic solvent, and disinfectant susceptibility tests, isoelectric focusing, detection of resistance determinants, plasmid profiling, pulsed-field gel electrophoresis (PFGE), and hybridization experiments. These isolates were compared to an outgroup consisting of 24 S. Saintpaul isolates obtained from humans and chickens in Germany and from poultry and poultry products (including turkeys) in Netherlands. A common core resistance pattern was detected for 27 German turkey and turkey product isolates. This pattern included resistance (full or intermediate) to ampicillin, amoxicillin-clavulanic acid, gentamicin, kanamycin, nalidixic acid, streptomycin, spectinomycin, and sulfamethoxazole and intermediate resistance or decreased susceptibility to ciprofloxacin (MIC, 2 or 1 mug/ml, respectively) and several third-generation cephalosporins (including ceftiofur and cefoxitin [MIC, 4 to 2 and 16 to 2 mug/ml, respectively]). These isolates had the same core resistance genotype, with bla(TEM-1), aadB, aadA2, sul1, a Ser83-->Glu83 mutation in the gyrA gene, and a chromosomal class 1 integron carrying the aadB-aadA2 gene cassette. Their XbaI, BlnI, and combined XbaI-BlnI PFGE patterns revealed levels of genetic similarity of 93, 75, and 90%, respectively. This study revealed that a multiresistant S. Saintpaul clonal line is widespread in turkeys and turkey products in Germany and was also detected among German human fecal and Dutch poultry isolates.

Evidence of class 1 integron transfer between Escherichia coli and Salmonella spp. on livestock farms

A study was conducted to determine if homologous integrons occurred in Escherichia coli and Salmonella spp. within livestock production sites in the United States and Thailand suggesting transfer of genetic resistance elements between those organisms. Fecal samples were collected via rectal swabs from live swine in the United States and Thailand, and cloacal swabs from live chickens in Thailand, and killed chickens at a U.S. abattoir. Isolates were derived only from farms harboring both Salmonella and E. coli, resulting in the inclusion of 571 E. coli and 98 Salmonella isolates derived from both livestock species in the United States and Thailand. Class 1 integron variable regions were detected using polymerase chain reaction targeting 5' and 3' conserved sequences. When integron-positive E. coli and Salmonella from the same farm had identical amplicon patterns, polymerase chain reaction products were sequenced to determine homology. Nine integron amplicons, with sizes ranging from 0.5 to 2.5 kb, were observed in bacterial isolates, and we found a single swine farm in Thailand from which identical amplicons were observed in both E. coli and Salmonella. Sequence analysis revealed a 1.0 kb amplicon common to both bacteria contained an aadA1 gene cassette encoding aminoglycoside 3'-adenyltransferase, conferring resistance to streptomycin and spectinomycin. A 2.0 kb amplicon was also found in both types of bacteria from that farm, containing an aadA5 gene encoding aminoglycoside 3'-adenyltransferase, an additional reading frame, orfD, with unknown function, and a dfrA17 gene encoding dihydrofolate reductase, conferring resistance to trimethoprim. Further analyses determined the amplicons were contained on plasmid DNA in both E. coli and Salmonella, and a plasmid of similar size was identified in both species and was found to harbor the class 1 integron. Our results indicate that while in most cases, integrons of coexisting E. coli and Salmonella differed, identical integron amplicons were found in those species from a single swine farm in Thailand, suggesting horizontal transfer between these two organisms may have occurred on-farm.

Clonal dissemination of the multi-drug resistant Salmonella enterica serovar Braenderup, but not the serovar Bareilly, of prevalent serogroup C1 Salmonella from Taiwan

Background

Nontyphoidal Salmonella is the main cause of human salmonellosis. In order to study the prevalent serogroups and serovars of clinical isolates in Taiwan, 8931 Salmonellae isolates were collected from 19 medical centers and district hospitals throughout the country from 2004 to 2007. The pulsed-field eletrophoresis types (PFGE) and antibiotic resistance profiles of Salmonella enterica serovars Bareilly (S. Bareilly) and Braenderup (S. Braenderup) were compared, and multi-drug resistance (MDR) plasmids were characterized.

Results

Over 95% of human salmonellosis in Taiwan was caused by five Salmonella serogroups: B, C1, C2-C3, D1, and E1. S. Typhymurium, S. Enteritidis, S. Stanley and S. Newport were the four most prevalent serovars, accounting for about 64% of isolates. While only one or two major serovars from four of the most prevalent serogroups were represented, four predominant serovars were found in serogroup C1 Salmonellae. The prevalence was decreasing for S. Choleraeuis and S. Braenderup, and S. Virchow and increasing for S. Bareilly. S. Braenderup mainly caused gastroenteritis in children; in contrast, S. Bareiley infected children and elderly people. Both serovars differed by XbaI-PFGE patterns. Almost all S. Bareilly isolates were susceptible to antibiotics of interest, while all lacked plasmids and belonged to one clone. Two distinct major clones in S. Braenderup were cluster A, mainly including MDR isolates with large MDR plasmid from North Taiwan, and cluster B, mainly containing susceptible isolates without R plasmid from South Taiwan. In cluster A, there were two types of conjugative R plasmids with sizes ranging from 75 to 130 kb. Type 1 plasmids consisted of replicons F1A/F1B, bla_TEM, IS26, and a class 1 integron with the genes dfrA12-orfF-aadA2-qacEΔ1-sulI. Type 2 plasmids belonged to incompatibility group IncI, contained tnpA-bla_CMY-2-blc-sugE genetic structures and lacked both IS26 and class 1 integrons. Although type 2 plasmids showed higher conjugation capability, type 1 plasmids were the predominant plasmid.

Conclusions

Serogroups B, C1, C2-C3, D1, and E1 of Salmonella caused over 95% of human salmonellosis. Two prevalent serovars within serogroup C1, S. Bareilly and cluster B of S. Braenderup, were clonal and drug-susceptible. However, cluster A of S. Braenderup was MDR and probably derived from susceptible isolates by acquiring one of two distinct conjugative R plasmids.

Association of virulence plasmid and antibiotic resistance determinants with chromosomal multilocus genotypes in Mexican Salmonella enterica serovar Typhimurium strains

Background

Bacterial genomes are mosaic structures composed of genes present in every strain of the same species (core genome), and genes present in some but not all strains of a species (accessory genome). The aim of this study was to compare the genetic diversity of core and accessory genes of a Salmonella enterica subspecies enterica serovar Typhimurium (Typhimurium) population isolated from food-animal and human sources in four regions of Mexico. Multilocus sequence typing (MLST) and macrorestriction fingerprints by pulsed-field gel electrophoresis (PFGE) were used to address the core genetic variation, and genes involved in pathogenesis and antibiotic resistance were selected to evaluate the accessory genome.

Results

We found a low genetic diversity for both housekeeping and accessory genes. Sequence type 19 (ST19) was supported as the founder genotype of STs 213, 302 and 429. We found a temporal pattern in which the derived ST213 is replacing the founder ST19 in the four geographic regions analyzed and a geographic trend in the number of resistance determinants. The distribution of the accessory genes was not random among chromosomal genotypes. We detected strong associations among the different accessory genes and the multilocus chromosomal genotypes (STs). First, the Salmonella virulence plasmid (pSTV) was found mostly in ST19 isolates. Second, the plasmid-borne betalactamase cmy-2 was found only in ST213 isolates. Third, the most abundant integron, IP-1 (dfrA12, orfF and aadA2), was found only in ST213 isolates. Fourth, the Salmonella genomic island (SGI1) was found mainly in a subgroup of ST19 isolates carrying pSTV. The mapping of accessory genes and multilocus genotypes on the dendrogram derived from macrorestiction fingerprints allowed the establishment of genetic subgroups within the population.

Conclusion

Despite the low levels of genetic diversity of core and accessory genes, the non-random distribution of the accessory genes across chromosomal backgrounds allowed us to discover genetic subgroups within the population. This study provides information about the importance of the accessory genome in generating genetic variability within a bacterial population.

Integron-containing bacteria in faeces of cattle from different production systems at slaughter

AIMS

To determine the prevalence and characteristics of integron-containing bacteria in faeces of cattle from grass-fed, lot-fed, or organically produced cattle.

METHODS AND RESULTS

Faecal samples from grass-fed (n = 125), lot-fed (n = 125) and organic (n = 135) cattle were tested for the presence of class 1 and class 2 integrons by using PCR and colony hybridisation. The prevalence of class 1 and class 2 integrase were higher in lot-fed cattle (71% and 62%) than grass-fed cattle (52% and 30%) which in turn were higher than organic cattle (25% and 11%). Isolation rates of integron-containing bacteria were reflective of PCR prevalence results.

CONCLUSIONS

The antimicrobial resistance genes harboured by the integrons differed little across the three systems and were typically to antimicrobials that would rarely be used therapeutically or for growth promotion purposes. The differences in prevalence observed between the systems may be a function of the intensiveness of each system.

SIGNIFICANCE AND IMPACT OF THE STUDY

Integron-containing bacteria may be present in all cattle production systems regardless of the amount of antimicrobial use and confirms that the prudent use of antimicrobials is required so that the development of integrons harbouring genes significant to human medicine is avoided.

Changes in antimicrobial resistance among Salmonella enterica subspecies enterica serovar Pullorum isolates in China from 1962 to 2007

There are few data available for the trends of antimicrobial resistance of Salmonella enterica subspecies enterica serovar Pullorum (S. Pullorum) in China and other parts of the world. Thus, the objective of this study was to evaluate the changes in antimicrobial resistance of S. Pullorum isolated from diseased chickens in China from 1962 to 2007. A total of 450 S. Pullorum isolates were tested for their susceptibility to 17 antimicrobials in a disk diffusion method. 39-95% of the isolates displayed a high level of resistance, particularly against ampicillin, carbenicillin, streptomycin, tetracycline, trimethoprim and sulfafurazole. Isolates exhibited increased resistance to carbenicillin, spectinomycin, trimethoprim, trimethoprim/sulfamethoxazole and nalidixic acid during the study period. Moreover, 56.2% of the isolates exhibited multiple drug resistance (MDR; resistance> or =4 antimicrobials) and showed an increasing trend between 1970-1979 and 2000-2007. Therefore, the results suggest that certain measures, including continued surveillance of antimicrobial resistance and the rational use of antimicrobials, are necessary and important in order to control the rapid increase in antimicrobial resistance in S. Pullorum.

Novel insertion sequence- and transposon-mediated genetic rearrangements in genomic island SGI1 of Salmonella enterica serovar Kentucky

Salmonella genomic island 1 (SGI1) is an integrative mobilizable element that harbors a multidrug resistance (MDR) gene cluster. Since its identification in epidemic Salmonella enterica serovar Typhimurium DT104 strains, variant SGI1 MDR gene clusters conferring different MDR phenotypes have been identified in several S. enterica serovars and classified as SGI1-A to -O. A study was undertaken to characterize SGI1 from serovar Kentucky strains isolated from travelers returning from Africa. Several strains tested were found to contain the partially characterized variant SGI1-K, recently described in a serovar Kentucky strain isolated in Australia. This variant contained only one cassette array, aac(3)-Id-aadA7, and an adjacent mercury resistance module. Here, the uncharacterized part of SGI1-K was sequenced. Downstream of the mer module similar to that found in Tn21, a mosaic genetic structure was found, comprising (i) part of Tn1721 containing the tetracycline resistance genes tetR and tet(A); (ii) part of Tn5393 containing the streptomycin resistance genes strAB, IS1133, and a truncated tnpR gene; and (iii) a Tn3-like region containing the tnpR gene and the beta-lactamase bla(TEM-1) gene flanked by two IS26 elements in opposite orientations. The rightmost IS26 element was shown to be inserted into the S044 open reading frame of the SGI1 backbone. This variant MDR region was named SGI1-K1 according to the previously described variant SGI1-K. Other SGI1-K MDR regions due to different IS26 locations, inversion, and partial deletions were characterized and named SGI1-K2 to -K5. Two new SGI1 variants named SGI1-P1 and -P2 contained only the Tn3-like region comprising the beta-lactamase bla(TEM-1) gene flanked by the two IS26 elements inserted into the SGI1 backbone. Three other new variants harbored only one IS26 element inserted in place of the MDR region of SGI1 and were named SGI1-Q1 to -Q3. Thus, in serovar Kentucky, the SGI1 MDR region undergoes recombinational and insertional events of transposon and insertion sequences, resulting in a higher diversity of MDR gene clusters than previously reported and consequently a higher diversity of MDR phenotypes.