Genetic characterisation of extended-spectrum β-lactamases in Escherichia coli isolated from retail chicken products including CTX-M-9 containing isolates: a food safety risk factor

1. Bacterial resistance to β-lactam antibiotics has risen dramatically in Escherichia coli from food animals. In a previous study, 29 randomly selected chicken products, collected in Portugal, were analysed for the presence of extended-spectrum β-lactamases (ESBLs)-producing E. coli; and during this study the genetic characterisation of ESBLs genes was investigated.

2. The presence of genes encoding TEM, OXA, SHV, and CTX-M type beta-lactamases was studied by PCR followed by sequencing. Additionally, other mechanisms of antimicrobial resistance, phylogenetic groups and the presence of virulence determinants were evaluated among the isolates.

3. β-lactamases genes were identified as follows: bla _CTX-M-14 (n?=?4), bla _CTX-M-1 (n?=?2), bla _CTX-M-9 (n?=?4) and bla _TEM-52 (n?=?13). Mutations at positions ?42, ?18, ?1, and +58 of ampC promoter region were identified in 4 non-ESBL-producing isolates. The tet(A) or tet(B) genes were identified in all tetracycline-resistant isolates; the aadA gene detected in 8 of 10 streptomycin-resistant isolates; the aac(3)-II gene in all gentamicin-resistant isolates; the cmlA gene in the chloramphenicol-resistant isolate; and sul1 and/or sul2 and/or sul3 genes were found in all trimethoprim-sulfamethoxazole-resistant isolates. The intI1 gene was detected in 8 trimethoprim-sulfamethoxazole-resistant isolates and the intI2 gene in 4 isolates; one gene cassette arrangements were identified among class 1 integrons (dfrA1?+?aadA1) and among the class 2 integrons (dfrA1?+?sat2?+?aadA1). Among cefotaxime-resistant isolates, 16 belonged to A or B1 phylogenetic groups, while 11 isolates were classified into the D or B2 phylogroups. At least one virulence-associated gene (aer, fimA, or papC) was detected in 74·1% of the cefotaxime-resistant isolates.

4. Because ESBLs-producing bacteria are resistant to a broad range of β-lactams, infections caused by these organisms complicate therapy and limit treatment options.     

Genomic Description of Antibiotic Resistance in Escherichia coli and Enterococci Isolates from Healthy Lusitano Horses

Antibiotic resistance is a global problem, and it is known that commensal bacteria can act as reservoir of antibiotic resistance genes of clinical importance. The aim of the present study was to determine the antibiotic resistance phenotype and mechanisms implicated in resistance of Escherichia coli and Enterococcus spp. isolates collected from fecal samples of 90 Lusitano horses from Portugal. Sixteen of the 71 E. coli isolates (22.5%) recovered showed resistance to at least one of the antibiotics tested. The number of E. coli isolates resistant to streptomycin, tetracycline, chloramphenicol, ampicillin, trimethoprim-sulfamethoxazole, and gentamicin was 9, 7, 6, 3, 2, and 1, respectively. The bla_TEM-1 and bla_OXA-1 genes were detected in ampicillin-resistant isolates and the sul2 and dfrA1 genes in trimethoprim-sulfamethoxazole-resistant, while the aac(3)-I, floR and tet(A) were found in the gentamicin, chloramphenicol and tetracycline-resistant isolates, respectively. Twenty-two of the 71 (31%) recovered enterococci showed antibiotic resistance for at least one of the tested antibiotics, and resistant isolates were identified as Enterococcus faecium (n = 14), E. faecalis (n = 3), E. hirae (n = 2), and Enterococcus spp. (n = 3). The erm(B) and erm(C) genes were identified in erythromycin-resistant enterococci and the tet(M) and/or tet(L) genes in tetracycline-resistant isolates. The slight prevalence of antibiotic resistance among commensal bacteria of healthy Lusitano horses can improve the treatment of upcoming infections in these horses because these microorganisms can be considered as antimicrobial indicator bacteria.     

食品动物源产CTX-M-14大肠杆菌传播分子机制的演变

从保存的2002-2009年分离的食品动物源大肠杆菌中,挑选16株bla_CTX-M-14阳性菌,用PCR方法检测超广谱β-内酰胺酶(ESBLs)编码基因、PMQR耐药基因及其他重要抗生素耐药基因(rmtB和floR);通过脉冲场凝胶电泳(PFGE)及种族进化关系分析16株细菌的亲缘关系;通过接合转移试验、复制子分型和bla_CTX-M-14上下游插入元件的检测,分析产CTX-M-14大肠杆菌的传播分子机制。PCR检测结果表明,16株食品动物源产CTX-M-14大肠杆菌大多属于系统发育组A组,其次为B1和D组,没有B2组;PFGE分型结果表明,同一时间内不同动物间存在产CTX-M-14共生型大肠杆菌克隆的扩散传播,但养殖场内CTX-M-14主要是随质粒或其他元件进行水平传播;质粒复制子分型结果表明,携带bla_CTX-M-14的质粒属于IncK(3/14)、 IncF(5/14)、 IncHI2(1/14)、IncFIB 和 IncF(1/14)、IncHI1和IncN(2/14)、 IncI1(2/14)等,且随着时间推移,复制子的种类呈增多趋势。2002-2007年的菌株bla_CTX-M基因的上下游均检测到ISEcp1和IS903;但2009年菌株除了部分在上下游都可以检测到ISEcp1和IS903外,还有的只检测到上游的ISEcp1或下游的IS903;2002-2009年的菌均未检测到ISCR1。16株产CTX-M-14大肠杆菌除了携带其他ESBLs编码基因,如bla_CTX-M79和bla_TEM-135外,还携带其他重要抗生素耐药基因,如oqxA、floR、aac(6')-1b-cr及rmtB,而且2002-2009年大肠杆菌携带耐药基因的种类和数量逐年增多;接合转移试验发现,2002-2005年的菌株,bla_CTX-M-14往往发生单独转移,而2009年分离菌bla_CTX-M-14往往和floR或rmtB位于同一质粒上发生共同转移。这说明养殖场使用氨基糖苷类或氟苯尼考等任何一种抗生素,都可以筛选出产CTX-M-14大肠杆菌并促进其扩散,所以动物养殖过程中要慎用这些抗生素。     

Phylogenetic groups and cephalosporin resistance genes of Escherichia coli from diseased food-producing animals in Japan

A total of 318 Escherichia coli isolates obtained from different food-producing animals affected with colibacillosis between 2001 and 2006 were subjected to phylogenetic analysis: 72 bovine isolates, 89 poultry isolates and 157 porcine isolates. Overall, the phylogenetic group A was predominant in isolates from cattle (36/72, 50%) and pigs (101/157, 64.3%) whereas groups A (44/89, 49.4%) and D (40/89, 44.9%) were predominant in isolates from poultry. In addition, group B2 was not found among diseased food-producing animals except for a poultry isolate. Thus, the phylogenetic group distribution of E. coli from diseased animals was different by animal species. Among the 318 isolates, cefazolin resistance (minimum inhibitory concentrations: ≥32 μg/ml) was found in six bovine isolates, 29 poultry isolates and three porcine isolates. Of them, 11 isolates (nine from poultry and two from cattle) produced extended spectrum β-lactamase (ESBL). The two bovine isolates produced bla_CTX-M-2, while the nine poultry isolates produced bla_CTX-M-25 (4), bla_SHV-2 (3), bla_CTX-M-15 (1) and bla_CTX-M-2 (1). Thus, our results showed that several types of ESBL were identified and three types of β-lactamase (SHV-2, CTX-M-25 and CTX-M-15) were observed for the first time in E. coli from diseased animals in Japan.     

Spread of extended-spectrum beta-lactamase producing Escherichia coli isolates in Swedish broilers mediated by an incI plasmid carrying blaCTX-M-1

Background

The already high and increasing occurrence of extended-spectrum beta-lactamases (ESBL) producing Escherichia coli in European broiler populations is of concern due to the fact that third and fourth generation cephalosporins are deemed critically important in human medicine. In Sweden 34% of the broilers carry ESBL/pAmpC producing E. coli in their gut, despite the absence of a known selection pressure such as antimicrobial usages. The aim of the current study was to characterise a selection of E. coli strains carrying the bla_CTX-M-1, to determine if the spread was due to a specific clone.

Findings

Ten isolates carrying bla_CTX-M-1 from Swedish broilers belonged to eight different multi-locus sequence types with three isolates belonging to ST155. The ST155 isolates were identical as assessed by PFGE. The bla_CTX-M-1 was in all isolates carried on a plasmid of replicon type incI, which also transferred resistance to tetracycline and sulfamethoxazole.

Conclusion

The occurrence of ESBL-producing E. coli in the Swedish broilers is not due to the emergence of a single clone, but rather the spread of a specific incI plasmid carrying bla_CTX-M-1.     

Genetic Characterization of Antibiotic Resistance in Enteropathogenic Escherichia coli Carrying Extended‐Spectrum β‐Lactamases Recovered from Diarrhoeic Rabbits

A total of 52 Escherichia coli strains isolated from diarrhoeic rabbits were investigated for their enteropathogenic E. coli (EPEC) pathotype by PCR amplification of eae and bfp virulence genes. A total of 22 EPEC isolates were identified, serotyped and studied for antibiotic resistance and screened for the detection of extended‐spectrum β‐lactamases (ESBLs). The EPEC isolates belonged to three serogroups (O26, O92 and O103). The most common serogroup (O103:K‐:H2) was observed among 17 EPEC strains, the O92:K‐serogroup in three isolates (the antibiotic sensitive ones) and the remaining O26:K‐serogroup in two isolates (the ESBLs isolates). Resistances to ampicillin and tetracycline were the most frequent and detected followed by resistance to nalidixic acid, streptomycin, trimethoprim–sulphamethoxazole, cefoxitin, gentamicin and ciprofloxacin. All the isolates were sensitive for amikacin, ceftazidime, aztreonam, imipenem, chloramphenicol, tobramycin and amoxicillin + clavulanic acid. Two isolates recovered from two adult animals showed an intermediate susceptibility to cefotaxime, and a positive screening test for ESBL was demonstrated in both. The bla_TEM gene was demonstrated in the majority of ampicillin‐resistant isolates. The aac(3)‐II or aac(3)‐IV genes were detected in the four gentamicin‐resistant isolates. In addition, the aadA gene was detected in 60% of streptomycin‐resistant isolates. The tet(A) or tet(B) genes were identified in all tetracycline‐resistant isolates. A total of nine EPEC isolates showed the phenotype SXT‐resistant, and the sul1 and/or sul2 and/or sul3 genes were detected in all of them. Our findings showed that the molecular detection by the eae and bfp genes by PCR followed by serotyping is useful for monitoring trends in EPEC infections of rabbits allowing the identification of their possible reservoirs. The detection of genes involved in the resistance to antibiotics of different families in a relatively high proportion of faecal E. coli isolates of rabbits is of great interest and could be considered a serious public health problem.     

Antimicrobial Resistance in Wildlife: Implications for Public Health

The emergence and spread of antimicrobial‐resistant (AMR) bacteria in natural environments is a major concern with serious implications for human and animal health. The aim of this study was to determine the prevalence of AMR Escherichia coli (E. coli) in wild birds and mammalian species. Thirty faecal samples were collected from each of the following wildlife species: herring gulls (Larus argentatus), black‐headed gulls (Larus ridibundus), lesser black‐back gulls (Larus fuscus), hybrid deer species (Cervus elaphus x Cervus nippon) and twenty‐six from starlings (Sturnus vulgaris). A total of 115 E. coli isolates were isolated from 81 of 146 samples. Confirmed E. coli isolates were tested for their susceptibility to seven antimicrobial agents by disc diffusion. In total, 5.4% (8/146) of samples exhibited multidrug‐resistant phenotypes. The phylogenetic group and AMR‐encoding genes of all multidrug resistance isolates were determined by PCR. Tetracycline‐, ampicillin‐ and streptomycin‐resistant isolates were the most common resistant phenotypes. The following genes were identified in E. coli: bla_TEM, strA, tet(A) and tet(B). Plasmids were identified in all samples that exhibited multidrug‐resistant phenotypes. This study indicates that wild birds and mammals may function as important host reservoirs and potential vectors for the spread of resistant bacteria and genetic determinants of AMR.     

Antimicrobial resistance in Escherichia coli isolates from frugivorous (Eidolon helvum) and insectivorous (Nycteris hispida) bats in Southeast Nigeria,with detection of CTX-M-15 producing isolates

Thirty-five Escherichia coli isolates obtained from the liver, spleen and intestines of 180 frugivorous and insectivorous bats were investigated for antimicrobial resistance phenotypes/genotypes, prevalence of Extended-Spectrum beta-lactamase (ESBL) production, virulence gene detection and molecular typing. Eight (22.9 %) of the isolates were multidrug resistant (MDR). Two isolates were cefotaxime-resistant, ESBL-producers and harbored the bla_CTX-M-15 gene; they belonged to ST10184-D and ST2178-B1 lineages. tet(A) gene was detected in all tetracycline-resistant isolates while int1 (n = 8) and bla_TEM (n = 7) genes were also found. Thirty-three of the E. coli isolates were assigned to seven phylogenetic groups, with B1 (45.7 %) being predominant. Three isolates were enteropathogenic E. coli (EPEC) pathovars, containing the eae gene (with the variants gamma and iota), and lacking stx1/stx2 genes. Bats in Nigeria are possible reservoirs of potentially pathogenic MDR E. coli isolates which may be important in the ecology of antimicrobial resistance at the human-livestock-wildlife-environment interfaces. The study reinforces the importance of including wildlife in national antimicrobial resistance monitoring programmes.     

Serogroup distribution,diversity of exotoxin gene profiles,and phylogenetic grouping of CTX-M-1- producing uropathogenic Escherichia coli

The emergence of CTX-M-1 producing Uropathogenic Escherichia coli (UPEC) has become a serious challenge. In addition to antimicrobial resistance, a number of virulence factors have been shown. Therefore, this study was designed to determine the prevalence of O- serogroups, phylogenetic groups, exotoxin genes, and antimicrobial resistance properties of CTX-M-1- producing UPEC. A total of 248 UPEC isolates were collected. The antibiotic resistance was performed, and PCR was used to detect the bla_CTX-M1, exotoxins, serogroups and phylogroups of UPEC. Of 248 isolates, 95 (38.3%) harbored bla_CTX-M-1. Of them, serogroups O1 and O25 were predominant, accounting for 20% and 13.7%, respectively. The hlyA was the dominant exotoxin gene (32.6%), followed by sat (28.4%), vat (22.1%), cnf (13.7%), picU (8.4%), and cdt (2.1%). The hlyA gene was significantly associated with pyelonephritis (P = 0.003). Moreover, almost half of the isolates (45.4%) belonged to phylogenetic group B2. Most of exotoxin genes were present in significantly higher proportions in group B2 isolates except cdt gene (P < 0.05). All of the isolates were susceptible to imipenem, nitrofurantoin, and fosfomycin. The CTX-M-1-producing UPEC strains causing nosocomial infections are more likely to harbor certain exotoxin genes, raising the possibility that this increase in virulence genes may result in an increased risk of complicated UTI.     

Characteristics of ciprofloxacin and cephalosporin resistant Escherichia coli isolated from turkeys in Great Britain

1. A field study was performed to investigate the presence and characteristics of ciprofloxacin-resistant, extended spectrum β-lactamase (ESBL) and AmpC Escherichia coli from turkeys in Great Britain. E. coli were isolated from ～9000 boot swab samples from 27 different farms owned by four different companies. Between 1 and 14 visits were made to each farm (mean 3) at between 0 and 15?m intervals (mean?～?5?m).

2. CHROMagar ECC with and without ciprofloxacin or cephalosporin antibiotics was used as selective isolation media. Representative isolates with different phenotypes were tested for mutations in gyrA and for: qnrA, B, S, qepA and aac(6′)-Ib genes, for ESBL phenotype, the presence of bla _CTX-M genes and plasmid type, and for ampC genes_. Representative ciprofloxacin-resistant and CTX-M isolates were further tested for serotype and PFGE type. On ciprofloxacin selective media 55% of samples yielded ciprofloxacin resistant E. coli and of those further analysed, most had ciprofloxacin MICs >4 mg/l and mutations in gyrA.

3. For the different companies, the mean number of samples per farm with cefoxitin- or cefotaxime-resistant isolates ranged from 1·0% to 61·9% and 4·7% to 31·7% respectively. Cefotaxime-resistance was most commonly associated with an ESBL phenotype, a CTX-M-1 or CTX-M-14 sequence type and an I1-γ or K plasmid inc type. The mechanism of cefoxitin resistance was not determined for most isolates, but where determined it was bla _CMY-2.

4. PFGE and serotyping showed clonally-related isolates persisting over multiple visits suggesting both more prudent use of antibiotics and improved farm hygiene are needed to address the issue of antimicrobial resistance in isolates from turkeys.     

Association between antimicrobial treatment and resistance of pathogenic Escherichia coli isolated from diseased swine in Kagoshima Prefecture,Japan

Pathogenic Escherichia coli is an important cause of diarrhea, edema disease, and septicemia in swine. In Japan, the volume of antimicrobial drugs used for animals is highest in swine, but information about the prevalence of antimicrobial-resistant bacteria is confined to apparently healthy animals. In the present study, we determined the O serogroups, virulence factors, and antimicrobial resistance of 360 E. coli isolates from swine that died of disease in Kagoshima Prefecture, Japan, between 1999 and 2017. The isolates of the predominant serogroups O139, OSB9, O149, O8, and O116 possessed virulence factor genes typically found in diarrheagenic E. coli. We further found five strains of third-generation cephalosporin-resistant E. coli that each produced an extended-spectrum β-lactamase encoded by bla_CTX-M-14, bla_CTX-M-15, bla_CTX-M-24, bla_CTX-M-61, or bla_SHV-12. In 218 swine with a clear history of antimicrobial drug use, we further analyzed associations between the use of antimicrobials for the treatment of diseased swine and the isolation of resistant E. coli. We found significant associations between antimicrobial use and selection of resistance to the same class of antimicrobials, such as the use of ceftiofur and resistance to cefotaxime, cefazolin, or ampicillin, the use of aminoglycosides and resistance to streptomycin, and the use of phenicols and resistance to chloramphenicol. A significant association between antimicrobial use and the resistance of E. coli isolates to structurally unrelated antimicrobials, such as the use of ceftiofur and resistance to chloramphenicol, was also observed.     

Diversity of Plasmids and Antimicrobial Resistance Genes in Multidrug‐Resistant Escherichia coli Isolated from Healthy Companion Animals

The presence and transfer of antimicrobial resistance genes from commensal bacteria in companion animals to more pathogenic bacteria may contribute to dissemination of antimicrobial resistance. The purpose of this study was to determine antimicrobial resistance gene content and the presence of genetic elements in antimicrobial resistant Escherichia coli from healthy companion animals. In our previous study, from May to August, 2007, healthy companion animals (155 dogs and 121 cats) from three veterinary clinics in the Athens, GA, USA area were sampled and multidrug‐resistant E. coli (n = 36; MDR, resistance to ≥2 antimicrobial classes) were obtained. Of the 25 different plasmid replicon types tested by PCR, at least one plasmid replicon type was detected in 94% (34/36) of the MDR E. coli; four isolates contained as many as five different plasmid replicons. Nine replicon types (FIA, FIB, FII, I2, A/C, U, P, I1 and HI2) were identified with FIB, FII, I2 as the most common pattern. The presence of class I integrons (intI) was detected in 61% (22/36) of the isolates with eight isolates containing aminoglycoside‐ and/or trimethoprim‐resistance genes in the variable cassette region of intI. Microarray analysis of a subset of the MDR E. coli (n = 9) identified the presence of genes conferring resistance to aminoglycosides (aac, aad, aph and strA/B), β‐lactams (ampC, cmy, tem and vim), chloramphenicol (cat), sulfonamides (sulI and sulII), tetracycline [tet(A), tet(B), tet(C), tet(D) and regulator, tetR] and trimethoprim (dfrA). Antimicrobial resistance to eight antimicrobials (ampicillin, cefoxitin, ceftiofur, amoxicillin/clavulanic acid, streptomycin, gentamicin, sulfisoxazole and trimethoprim‐sulfamethoxazole) and five plasmid replicons (FIA, FIB, FII, I1 and I2) were transferred via conjugation. The presence of antimicrobial resistance genes, intI and transferable plasmid replicons indicate that E. coli from companion animals may play an important role in the dissemination of antimicrobial resistance, particularly to human hosts during contact.     

Low Occurrence of Extended‐Spectrum β‐lactamase‐Producing Escherichia coli in Finnish Food‐Producing Animals

ESBL/AmpC‐producing Escherichia coli is increasingly isolated from humans and animals worldwide. The occurrence of ESBL/AmpC‐producing E. coli was studied in food‐producing animals in Finland, a country with a low and controlled use of antimicrobials in meat production chain. A total of 648 cattle, 531 pig, 495 broiler and 35 turkey faecal samples were collected from four Finnish slaughterhouses to determine the presence of extended‐spectrum β‐lactamase (ESBL/AmpC)‐producing E. coli. In addition, 260 broiler and 15 turkey samples were screened for carbapenemase‐producing E. coli. Susceptibility to different class of cephalosporins and meropenem was determined with disc diffusion tests according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Determination of ESBL/AmpC production was performed with a combination disc diffusion test according to the recommendations of the European Food Safety Authority (EFSA). Plasmidic bla_ESBL/AmpC genes were characterized by polymerase chain reaction and sequencing. A collection of isolates producing AmpC enzyme but not carrying plasmidic bla_AmpC was analysed by PCR and sequencing for possible chromosomal ampC promoter area mutations. Altogether ESBL/AmpC‐producing E. coli was recovered from five cattle (0.8%), eight pig (1.5%) and 40 broiler samples (8.1%). No ESBL/AmpC‐producing E. coli was found in turkey samples. Carbapenem resistance was not detected. Altogether ESBL/AmpC‐producing E. coli was found on 4 (2.0%), 3 (4.5%) and 14 (25%) cattle, pig and broiler farms, respectively. From cattle samples 3 (27%) bla_CTX‐M‐1 and from broiler samples 13 (33%) bla_CTX‐M‐1 and 22 (55%) bla_CMY‐2 gene‐carrying isolates were detected. In pigs, no plasmidic bla_ESBL/AmpC gene‐carrying isolates were found. In all analysed isolates, the same mutations in the promoter region of chromosomal ampC were detected. The results showed low occurrence of ESBL/AmpC‐producing E. coli in Finnish food‐producing animals. In pigs, plasmidic bla_ESBL/AmpC‐carrying E. coli was not detected at all.     

Characterisation of ceftiofur resistance in swine bacterial pathogens

A PCR based method was developed for the identification of ceftiofur resistance genes (bla_CMY-2, bla_TEM-1, and ampC) in swine bacterial pathogens. Using this method, the ceftiofur resistant (n = 76) and susceptible (n = 45) strains of Bordetella bronchiseptica, Salmonella spp., Escherichia coli, and Pasteurella multocida were screened for the presence of these three genes. The resistant genes were detected in 70% (bla_TEM-1), 68% (bla_CMY-2) and 45% (ampC) of the resistant isolates and in 18% (bla_TEM-1), 27% (bla_CMY-2), and 36% (ampC) of the susceptible isolates. Results obtained in the present study showed widespread distribution of these three resistance genes in ceftiofur-resistant swine pathogens. It was also observed that more pathogens are acquiring these resistance genes.     

Clinically relevant multidrug resistant Salmonella enterica in swine and meat handlers at the abattoir

The presence of multidrug resistant (MDR) Salmonella serotypes in slaughtered swine, carcasses, meat and meat handlers is scarcely evaluated. Recently we demonstrated that diverse Salmonella serotypes are frequently present in swine, pork meat and carcasses, and meat handlers at Portuguese abattoirs. Here we have characterized their antibiotic resistance phenotypes and genotypes, helping elucidate the flow of MDR Salmonella in the food chain. Testing 60 Salmonella isolates from different serotypes, the highest frequencies of resistance were observed for tetracycline (T) [70% (n = 42/60), tet(A)/tet(B)/tet(G)], streptomycin (S) [63% (n = 38/60), aadA2/strA/strB], sulfamethoxazole (Sul) [62% (n = 37/60), sul1/sul2/sul3] and ampicillin (A) [57% (n = 34/60), bla_PSE-1/bla_TEM]. Thirty-seven percent (n = 22/60) carried class 1 integrons and multidrug resistance was frequently observed (63% n = 38/60), including those serotypes common to human infections [S. Typhimurium 78% n = 25/32; S. 4,[5],12:i:- 67% n = 2/3; S. Rissen 75% (n = 3/4); S. London 67% n = 2/3; S. Derby 55%; n = 6/11)]. The emergent S. 4,[5],12:i:- isolates were mostly characterized by ASSuT phenotype [bla_TEM/strA-strB/sul2/tet(B)], typical of the European clone, while for the first time the ST phenotype [strA-strB-tet(A)-tet(B)] was also observed. Moreover, we report a first finding of a MDR phenotype in S. London [ANSSuT; bla_TEM-strA-strB-sul2-tet(A)]. Our findings suggest that the abattoir environment and the slaughter operations seem not only to harbor MDR serotypes that originated in the pig reservoir, but also propagate them through cross-contamination processes, involving meat handlers. The present study suggests a probable relationship between swine and human salmonellosis throughout the food chain, which is of interest for epidemiological, animal health and public health purposes.     

Detection of multidrug resistant Escherichia coli in the ovaries of healthy broiler breeders with emphasis on extended-spectrum β-lactamases producers

In the last few years, antimicrobial resistant (AMR) Escherichia coli have been detected in newborn chickens suggesting their vertical transmission from breeding birds to their offspring. However, little is known about the presence of AMR E. coli in the reproductive organs of broiler breeders. The aim of this study was to investigate the presence of E. coli in the ovaries of healthy broiler breeders and to study their antimicrobial resistance. Samples from broiler breeders (n = 80) collected from 80 different broiler breeder flocks were included in this study. Antibiotic susceptibility testing was performed using disk diffusion method according to Clinical and Laboratory Standards Institute guidelines. Minimal inhibitory concentrations (MICs) of five antimicrobial agents were determined by Etest. PCR and sequencing were used to detect the bla_ESBL genes. E. coli were detected in the ovaries of thirty seven out of 80 (46.25%) sampled flocks. High levels of resistance to various first-line antimicrobial agents were recorded in E. coli isolates. This study showed that 89.18% of E. coli isolates were multidrug resistant (MDR). Furthermore, MDR extended-spectrum β-lactamases (ESBL)-producing E. coli were detected in the ovaries of four different broiler breeder flocks. Molecular characterization revealed that three isolates harboured bla_CTX-M-1 gene and one isolate expressed bla_SHV-12 gene. In addition, one bla_CTX-M-1 -producing E. coli co-harboured the bla_TEM-1 gene. These findings would contribute to a better epidemiological understanding of MDR E. coli for improve existing preventive strategies in order to reduce the dissemination of antimicrobial resistance in the broiler production system.     

Antimicrobial resistance of Escherichia coli isolates from canine urinary tract infections

This study determined the antimicrobial resistance profiles of Escherichia coli isolates from dogs with a presumptive diagnosis of urinary tract infection (UTI). Urine samples from 201 dogs with UTI diagnosed through clinical examination and urinalysis were processed for isolation of Escherichia coli. Colonies from pure cultures were identified by biochemical reactions (n=114) and were tested for susceptibility to 18 antimicrobials. The two most frequent antimicrobials showing resistance in Urinary E. coli isolates were oxytetracycline and ampicillin. Among the resistant isolates, 17 resistance patterns were observed, with 12 patterns involving multidrug resistance (MDR). Of the 69 tetracycline-resistant E. coli isolates, tet(B) was the predominant resistance determinant and was detected in 50.9% of the isolates, whereas the remaining 25.5% isolates carried the tet(A) determinant. Most ampicillin and/or amoxicillin-resistant E. coli isolates carried bla_TEM-1 genes. Class 1 integrons were prevalent (28.9%) and contained previously described gene cassettes that are implicated primarily in resistance to aminoglycosides and trimethoprim (dfrA1, dfrA17-aadA5). Of the 44 quinolone-resistant E. coli isolates, 38 were resistant to nalidixic acid, and 6 were resistant to nalidixic acid, ciprofloxacin and enrofloxacin. Chromosomal point mutations were found in the GyrA (Ser83Leu) and ParC (Ser80Ile) genes. Furthermore, the aminoglycoside resistance gene aacC2, the chloramphenicol resistant gene cmlA and the florfenicol resistant gene floR were also identified. This study revealed an alarming rate of antimicrobial resistance among E. coli isolates from dogs with UTIs.     

Circulation of emerging NDM‐5‐producing Escherichia coli among humans and dogs in Egypt

The emergence of NDM‐producing Escherichia coli has considerably threatened human and animal health worldwide. This study describes for the first time in Egypt, the draft genome sequences of emerging NDM‐5‐producing E. coli from humans and dogs, and investigates genetic relatedness between isolates from both sources. Two E. coli from human urine and seven from environmental clinical samples of dogs exhibited resistance to carbapenems and harbouring bla_NDM were subjected to Illumina Miseq whole‐genome sequencing (WGS). Assembly and analysis of the reads were performed to identify resistance genes, multilocus sequence types (MLST), plasmid replicon types (Inc) and insertion sequences (IS) of the bla_NDM region; core genome MLST (cgMLST) analysis was also performed. Two different NDM alleles were identified; bla_NDM‐5 in E. coli HR119 from the urine of a healthy person and environmental samples of dogs, and bla_NDM‐1 in E. coli HR135 from a human patient's urine. Multiple mobilizable resistance genes to different antimicrobial classes were identified except the colistin resistance gene, mcr. E. coli isolates from humans and dogs were assigned to different sequence types (STs). Using cgMLST, dog isolates clustered together with only 1–2 allellic differences; however, human E. coli showed 1,978 different allelles compared with dog isolates. Plasmidfinder results indicated the presence of an IncX3 replicon in bla_NDM‐5‐producing E. coli; however, bla_NDM‐1 was linked to IncCoIKP3. Notably, the NDM region (3 Kb) in all isolates from humans and dogs was highly similar with variable flanking sequences that represented different IS elements. This study reports the first emergence of NDM‐5‐producing E. coli from dogs in Egypt that shared some genetic features with human isolates and could be considered potential public health threats.     

Antimicrobial resistance in faecal Escherichia coli isolates from farmed red deer and wild small mammals. Detection of a multiresistant E. coli producing extended-spectrum beta-lactamase

Eighty-nine Escherichia coli isolates recovered from faeces of red deer and small mammals, cohabiting the same area, were analyzed to determine the prevalence and mechanisms of antimicrobial resistance and molecular typing. Antimicrobial resistance was detected in 6.7% of isolates, with resistances to tetracycline and quinolones being the most common. An E. coli strain carrying bla_CTX-M-1 as well as other antibiotic resistant genes included in an unusual class 1 integron (Intl1-dfrA16–bla_PSE-1-aadA2-cmlA1-aadA1-qacH-IS440-sul3-orf1-mef(B)Δ-IS26) was isolated from a deer. The bla_CTX-M-1 gene was transferred by conjugation and transconjugants also acquired an IncN plasmid. This strain was typed as ST224, which seems to be well adapted to both clinical and environmental settings. The phylogenetic distribution of the 89 strains varied depending on the animal host. This work reveals low antimicrobial resistance levels among faecal E. coli from wild mammals, which reflects a lower selective pressure affecting these bacteria, compared to livestock. However, it is remarkable the detection of a multi-resistant ESBL-E. coli with an integron carrying clinically relevant antibiotic-resistance genes, which can contribute to the dissemination of resistance determinants among different ecosystems.