Pathogenome comparison and global phylogeny of Escherichia coli ST1485 strains.

Escherichia coli ST1485 strains belong to the clinically important phylogroup F and have disseminated worldwide in humans, animals, and the environment. Here, we elucidated the pathogenome of a global collection of E. coli ST1485 isolates from diverse sources retrieved from public databases and a high-quality sequenced complete genome of colistin-resistant E. coli strain CFSAN061771 isolated from raw milk cheese which designated as a reference strain. CFSAN061771 belongs to O83:H42-ST1485 pathotype and carries a conjugative ColV plasmid, pCFSAN061771_01, combining extraintestinal virulence genes (ompt, sitA, iroN, etsC, traT, cvaC, hylF, iss, tsh, mchf, iucC, iutA) with a multidrug resistance island (blaTEM-1, aph(6)-Id, aph(3″)-Ib, sul2, dfrA14). Comparative genomic analysis revealed a high frequency of pCFSAN061771_01-like plasmids in E. coli ST1485. A notable evolutionary genetic event in E. coli ST1485 strains is the acquisition of a pCFSAN061771_02-like plasmid, which confers resistance to several antimicrobials, tellurium, and quaternary ammonium compounds. The identical virulence and antibiotic resistance profiles identified in some human and animal strains are worrisome. This is the first study to emphasize the significance of E. coli ST1485 as a global high-risk virulent and multidrug-resistant clone with zoonotic potential.

Loads of Coliforms and Fecal Coliforms and Characterization of Thermotolerant Escherichia coli in Fresh Raw Milk Cheese.

The aim of this study was to assess the hygienic status of raw milk cheese and determine the trends of virulence and antimicrobial resistance in thermotolerant Escherichia coli. Two hundred samples of karish, a popular Egyptian fresh raw milk cheese, were analyzed for coliforms and fecal coliforms using a standard most probable number (MPN) technique. Overall, 85% of samples were unsuitable for consumption, as they exceeded Egyptian standards for coliforms (10 MPN/g), and 65% of samples exhibited coliforms at 44.5 °C. Of 150 recovered thermotolerant strains, 140 (93.3%) were identified as E. coli. Importantly, one Shiga toxin-producing E. coli (STEC) strain carrying a striking virulence pattern, stx1-, stx2+, eae-, was detected. Eleven strains (7.8%, 11/140) showed resistance to third-generation cephalosporins. Antibiotic resistance genes included blaSHV, blaCTX-M, qnrS, tet(A), and tet(B), which were present in 4.3%, 2.8%, 0.71%, 2.1%, and 0.71% of isolates, respectively. In conclusion, this study indicated that hygienic-sanitary failures occurred throughout the production process of most retail karish cheese. Furthermore, our findings emphasize the need for adopting third-generation cephalosporin-resistant E. coli as an indicator for monitoring antimicrobial resistance in raw milk cheese to identify the potential public health burden associated with its consumption.

Occurrence, Phenotypic and Molecular Characteristics of Vancomycin-Resistant Enterococci Isolated from Retail Raw Milk in Egypt.

The aim of this study was to determine the occurrence, phenotypic and molecular characteristics of vancomycin-resistant enterococci (VRE), isolated from retail raw cow's milk. One hundred milk samples collected from retail shops in Egypt were examined for the occurrence of VRE by using kanamycin aesculin azide agar supplemented with 4 µg/mL vancomycin. PCR was conducted to determine enterococcal species and to screen the isolated strains for the presence of antibiotic resistance and virulence genes. All isolated strains were characterized by antimicrobial susceptibility testing for 12 antibiotics. From 24 samples (24%), we recovered 22 isolates (91.6%) classified as VRE (minimum inhibitory concentration ≥32) and 2 isolates (8.3%) classified as intermediate resistant to vancomycin (≤16). Enterococcus faecium (29.1%), Enterococcus faecalis (12.5%), Enterococcus casseliflavus (16.6%), and Enterococcus gallinarum (4.1%) were identified by using multiplex PCR. The genus Enterococcus was resistant to clindamycin (100%), linezolid (91.6%), teicoplanin (91.6%), erythromycin (87.5%), and tetracycline (29.1%). Co-resistance to vancomycin, teicoplanin, and linezolid was detected in 83.3% of isolates. Antibiotic resistance genes vanB, tet(M), tet(L), and erm(B) were identified in 29.1%, 16.6%, 8.3%, and 4.1% of isolates, respectively. Virulence genes gelE and esp were detected in 16.6% and 12.5% of isolates, respectively. In conclusion, the high occurrence of co-resistance to vancomycin, teicoplanin, and linezolid reported in this study is alarming. The high frequency of linezolid resistance prompts increased the attention of researchers to routinely perform linezolid susceptibility in food isolates. This study declares potential food safety risks from consumption and improper handling of raw milk regarding clinically important bacteria and promotes necessary legislation for forbidding the selling and consumption of retail raw milk.

Toxigenic Potential of Bacillus cereus Strains Isolated from Retail Dairy Products in Egypt.

Little is known about the virulence in Bacillus cereus strains isolated from retail dairy products in the Middle East and particularly from Egypt. In this study, the occurrence of B. cereus in 290 samples of dairy products (raw milk, Ras cheese, pasteurized extended shelf life [ESL] milk) collected from retail shops was investigated. The potential of 126 selected isolates of B. cereus to possess genes encoding nonhemolytic enterotoxin, hemolysin BL, and cytotoxin K (cytK), and to grow at 7°C was verified. The highest occurrence of B. cereus was found in raw milk (85%, 85/100) followed by Ras cheese (10%, 10/100) and ESL milk samples (8.8%, 8/90). A large proportion of the B. cereus isolates from raw milk (48.9%, 48/99) and Ras cheese (71.4%, 10/14) had at least one complete set of toxin genes (nhe or hbl). Enterotoxin genes, nheA, nheB, nheC, hblA, hblD, and hblC, were detected in 38.4% (5/13), 53.8% (7/13), 61.5% (8/13), 46.1% (6/13), 46.1% (6/13), and 23.1% (3/13) of ESL milk isolates, respectively. cytK was identified in 42.4% (42/99), 50% (7/14), and 46.2% (6/13) of raw milk, Ras cheese, and ESL milk isolates, respectively. The psychrotrophic ability was observed in 22.2% and 15.3% of isolates recovered from raw milk and ESL milk, respectively. The toxigenic potential of B. cereus strains described in this study may pose a health risk to the consumer and, therefore, the presence of these bacteria in retail dairy products should be monitored to ensure consumers' safety.

Genomic features of colistin resistant Escherichia coli ST69 strain harboring mcr-1 on IncHI2 plasmid from raw milk cheese in Egypt.

There is emerging evidence that food of animal origin may be responsible for the spread of multidrug resistant extraintestinal pathogenic Escherichia coli in the community. Here, we describe the emergence of colistin resistance gene, mcr-1, in a strain belonging to the dominant uropathogenic E. coli ST69 lineage. E. coli strain CFSAN061770 was isolated during monitoring of the popular Egyptian raw milk cheese, karish cheese, for the presence of colistin resistance. The complete genome of E. coli strain CFSAN061770 comprises a chromosome of 5,292,297 bp with a G + C content of 50.6%. Further, three plasmids named pEGY1-MCR-1, pEGY2 and pEGY3 of 228,947 bp, 103,234 bp and 87,012 bp were detected, respectively. Plasmid pEGY1-MCR-1 belongs to the IncHI2 incompatibility group and carries the colistin resistance mcr-1 gene flanked by two ISApl1 elements and forms a composite transposon. It mediates resistance to aminoglycosides (aadA1 and aadA2), phenicol (cmlA1 and floR), sulfonamides (sul3), and tetracycline (tet(A)), and these loci were found clustered in a multidrug resistant region. Plasmid pEGY3 carries a complex multiple resistance locus (CMR) (aph(3')-Ia, strA, strB, sul2, and blaTEM-1) encoding resistance to different classes of antibiotics. Interestingly, the closest plasmids to plasmid pEGY1-MCR-1 detected from the NCBI Blast search belonged to the incompatibility group IncHI2 and were from the Kingdom of Saudi Arabia and Qatar which suggests a dissemination of pEGY1-MCR-1-like plasmids in the Middle East. Most striking, and of great public health concern is that strain CFSAN061770 carries five virulence genes (iss, fimH, iutA, kpsMIII and kpsTIII) which were identified in clinical extraintestinal pathogenic E. coli. Besides that, it carries the astA gene, which codes for the enteroaggregative E. coli heat-stable toxin 1 (EAST1).

Molecular and Phenotypic Analysis of Hemolytic Aeromonas Strains Isolated from Food in Egypt Revealed Clinically Important Multidrug Resistance and Virulence Profiles.

The aim of this study was to determine the public health significance of hemolytic Aeromonas species isolated from 213 food samples in Egypt, based on their virulence and antimicrobial-resistance potential. We recovered 63 strains, isolated from fish, raw milk, karish cheeses, and ras cheese in 29 (31.18%) of 93, 10 (25.00%) of 40, 13 (32.50%) of 40, and 11 (27.50%) of 40 samples, respectively. The most prevalent virulence gene was alt (50.79%), followed by aerA (34.92%), asa1 (39.68%), ahh1 (20.63%), act (11.11%), and ast (3.17%). Thirteen strains screened in this study carried no hemolysin gene, but only the alt gene, and another eight hemolytic strains screened, carried no virulence gene. The virulence signatures " ahh1+ aerA" and " alt+ act," in which the genes interact synergistically to induce severe diarrhea, were detected in two and four strains, respectively. Most showed resistance to third-generation cephalosporins, aztreonam, and imipenem, which indicates the complexity of the ß-lactamase production in our hemolytic Aeromonas strains. Fourteen (22.22%) of 63 strains carried one or more antimicrobial-resistance markers, including the blaCTX-M, blaTEM, tet(A), tet(E), and intI1 genes, which were detected in 6.34, 3.17, 3.17, 4.76, and 14.28% of isolates, respectively. In conclusion, the majority of hemolytic Aeromonas strains isolated from the intestinal contents of healthy fish and naturally contaminated milk and cheeses were not commensal but had developed multidrug-resistance and virulence profiles, indicating an emerging potential health risk. Importantly, screening for certain hemolysin genes may not be reliable in predicting the pathogenic potential of Aeromonas species and, thereby, the safety of analyzed foods. Our findings indicate that specific criteria are required for the phenotypic and molecular analysis of Aeromonas species in food items, particularly those eaten without further treatment, to ensure their safety.

Biodegradation of Chlorpyrifos, Malathion, and Dimethoate by Three Strains of Bacteria Isolated from Pesticide-Polluted Soils in Sudan.

This study was done to identify pesticide-biodegrading microorganisms and to characterize degradation rates. Bacillus safensis strain FO-36bT, Bacillus subtilis subsp. inaquosorum strain KCTC13429T, and Bacillus cereus strain ATCC14579T were isolated from pesticide-polluted soil in Sudan, separately incubated with each pesticide with periodic samples drawn for GC and GC-MS. Pesticide biodegradation followed a biphasic model. α and ß half-lives (days) of chlorpyrifos, malathion, and dimethoate in B. safensis culture were 2.13, 4.76; 2.59, 5.66; and 9.5, 11.0, respectively. Values in B. subtilis and B. cereus cultures were 4.09, 9.45 and 4.33, 9.99 for chlorpyrifos; 2.99, 5.36 and 2.43, 4.71 for malathion; and 9.53, 15.11 and 4.16, 9.27 for dimethoate. No metabolite was detected in B. subtilis cultures, whereas a few were detected from B. safensis and B. cereus cultures. Bacterial efficiency can be ordered as B. safensis > B. subtilis > B. cereus for chlorpyrifos and B. cereus > B. subtilis > B. safensis for malathion and dimethoate.

Levels of organochlorine pesticides in the blood of people living in areas of intensive pesticide use in Sudan.

Ninety-six human blood samples were collected from six locations that represent areas of intensive pesticide use in Sudan, which included irrigated cotton schemes (Wad Medani, Hasaheesa, Elmanagil, and Elfaw) and sugarcane schemes (Kenana and Gunaid). Blood samples were analyzed for organochlorine pesticide residues by gas liquid chromatography (GLC) equipped with an electron capture detector (ECD). Residues of p,p'-dichlorodiphenyldichloroethylene (DDE), heptachlor epoxide, γ-HCH, and dieldrin were detected in blood from all locations surveyed. Aldrin was not detected in any of the samples analyzed, probably due to its conversion to dieldrin. The levels of total organochlorine burden detected were higher in the blood from people in the irrigated cotton schemes (mean 261 ng ml(-1), range 38-641 ng ml(-1)) than in the blood of people from the irrigated sugarcane schemes (mean 204 ng ml(-1), range 59-365 ng ml(-1)). The highest levels of heptachlor epoxide (170 ng ml(-1)) and γ-HCH (92 ng ml(-1)) were observed in blood samples from Hasaheesa, while the highest levels of DDE (618 ng ml(-1)) and dieldrin (82 ng ml(-1)) were observed in blood samples from Wad Medani and Kenana, respectively. The organochlorine levels in blood samples seemed to decrease with increasing distance from the old irrigated cotton schemes (Wad Medani, Hasaheesa, and Elmanagil) where the heavy application of these pesticides took place historically.

The fear of using tramadol for pain control (tramadolophobia) among Egyptian patients with cancer.

OBJECTIVES: The fear of using tramadol for pain control (tramadolophobia) by Egyptian patients with cancer is a frequent problem in our practice. This study was conducted to explore the prevalence of and the reasons behind tramadolophobia among Egyptian patients with cancer. METHODS: A structured interview including open-ended and closed questions. The study included 178 adult patients with cancer from two cancer centers in Cairo and Sharkia, Egypt. RESULTS: The source of information about tramadol was a non-healthcare-related source in 168 (94 percent) patients, mainly the media (50 percent). The believed uses of tramadol were abuse related in 94 (53 percent) patients, stimulant (physical, sexual, and to boost alertness) in 59 (33 percent), and analgesic in 55 (31 percent). Twenty-six (15 percent) patients gave history of tramadol use, largely (69 percent) as a stimulant. In case tramadol was prescribed for pain control, 90 (51 percent) patients refused to take it, 59 (33 percent) patients agreed to take it with concern about addiction, and only 29 (16 percent) patients agreed without concerns. Among those who refused taking tramadol for pain, the mentioned reason of refusal was addiction-related fears in 57 percent. CONCLUSIONS: The stigmatization and misconceptions about tramadol may have resulted in tramadolophobia among the majority of Egyptian patients with cancer. This further complicates the barriers to cancer pain control in Egypt. Being the only available World Health Organization step-II analgesic in Egypt, interventions to overcome tramadolophobia should be taken.

Genetic characterization of antibiotic resistance and virulence factors in Enterococcus spp. from Japanese retail ready-to-eat raw fish.

Little information is available on the diversity and distribution of resistance and virulence factors in enterococci isolated from retail fish. In this study, 200 samples of retail ready-to-eat raw fish (sashimi) collected from the Japanese prefecture of Hiroshima were analyzed for incidence of Enterococcus spp. We recovered 96 enterococcal isolates from 90 (45%, 90/200) samples. Fifty-six strains were identified at the species level: E. faecalis (n = 31), E. faecium (n = 7), E. casseliflavus (n = 7), E. gallinarum (n = 3), E. phoeniculicola (n = 4), E. raffinosus (n = 2), E. saccharolyticus (n = 1), and E. gilvus (n = 1). Twenty-five (26%, 25/96) strains carried antibiotic resistance genes. These included the tet(M), tet(L), tet(K), erm(B), msr(A/B), aph(3'), and blaZ genes, which were detected in 12.5%, 9.3%, 2%, 14.5%, 1%, 1%, and 2% of isolates, respectively. The virulence genes gelE and asa1 were detected in 31 and 24 E. faecalis strains, respectively. Both genes were detected in one E. faecium strain. In conclusion, this is the first study to underscore the importance of sashimi as not only a reservoir of Enterococcus spp. carrying resistance and virulence genes, but also a reservoir for unusual Enterococcus spp.

The use of opioids at the end-of-life and the survival of Egyptian palliative care patients with advanced cancer.

BACKGROUND AND AIM: One of the barriers to cancer pain control and palliative care (PC) development is the misconception that the use of opioids may hasten death. This concern is exaggerated when higher doses of opioids are used at the end-of-life. The aim of this study was to investigate the relationship between survival and the dose of opioids used at the end-of-life of patients with advanced cancer in an Egyptian PC setting. METHODS: Retrospective review of the medical records of 123 patients with advanced cancer managed in an Egyptian cancer center-based palliative medicine unit (PMU). Patients were classified according to the last prescribed regular opioid dose expressed in milligrams of oral morphine equivalent (OME) per day (mg OME/24 h) into three groups: no opioid or low-dose group (<120 mg OME/24 h), intermediate-dose group (120-<300 mg OME/24 h) and high-dose group (≥300 mg OME/24 h). Survival was calculated from the date of first referral to the PMU to death. RESULTS: The median age of patients was 53 years, breast cancer was the most common diagnosis (18%) and the majority (68%) died at home. Opioids were prescribed for pain control in 94% of patients and were prescribed on regular basis in 89%. The mean last prescribed opioid dose for the whole group of patients was 167 (±170) mg OME/24 h and it was highest among patients with pleural mesothelioma [245 (±258) mg OME/24 h]. The last prescription included no opioids or low-dose opioids in 57 (46%) patients, intermediate-dose in 42 (34%) and high-dose in 24 (20%). The estimated median survival was 45 days for the no opioid/low-dose group, 75 days for the intermediate-dose group and 153 days for the high-dose group (P=0.031). CONCLUSIONS: The results suggest that the dose of opioids has no detrimental impact on the survival of patients with advanced cancer in an Egyptian PC setting. Further research is needed to overcome barriers to cancer pain control especially in settings with inadequate cancer pain control.

Occurrence and characteristics of methicillin-resistant and -susceptible Staphylococcus aureus and methicillin-resistant coagulase-negative staphylococci from Japanese retail ready-to-eat raw fish.

Staphylococci are not part of the normal fish microflora. The presence of staphylococci on fish is an indication of (a) post-harvest contamination due to poor personnel hygiene, or (b) disease in fish. The aim of this study was to determine the prevalence, molecular genetic characteristics, antibiotic resistance and virulence factors of methicillin-susceptible Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS) isolated from 200 samples of retail ready-to-eat raw fish (sashimi) collected from the Japanese prefecture of Hiroshima. We characterized 180 staphylococcal strains. A majority of the grocery stores surveyed (92%, 23/25) contained fish contaminated with Staphylococcus species. We recovered 175 S. aureus isolates from 174 (87%, 174/200) samples, with 170 isolates of MSSA. For the MRSA and MR-CoNS, 10 isolates were obtained from 10 samples (5%, 10/200) collected from 10 shops (40%, 10/25) belonging to four supermarket chains. SCCmec typing revealed the presence of a type IV.1 SCCmec cassette in S. warneri isolates, a type II.1 SCCmec cassette in S. haemolyticus isolates and a cassette in methicillin-resistant S. aureus (MRSA) isolates that could not be typed. Molecular typing of two MRSA isolates by spa sequencing and multilocus sequence typing (MLST) identified t1767 and ST8, respectively. Antibiotic resistance genes that confer resistance to aminoglycosides, tetracyclines, ß-lactams, macrolides, lincosamides and streptogramin B (MLS(B)) antibiotics were detected. Genes encoding one or more of the following virulence factors: staphylococcal enterotoxins (seb, and sed), toxic shock syndrome toxin 1 (tst), exfoliative toxin (etaA) were detected in 14.2% (25/175) of S. aureus isolates. The accessory gene regulator (agr) typing of S. aureus isolates revealed that agr type 1 was most prevalent (96.5%, 169/175) followed by type 2 (2.2%, 4/175) and type 3 (1.1%, 2/175). None of the S. aureus isolates carried the Panton-Valentine leucocidin (PVL) encoding genes, lukF-PV and lukS-PV. To the best of our knowledge, this is the first report to show MRSA and MR-CoNS isolated from retail ready-to-eat food in Japan. Our results showed that sashimi is a likely vehicle for transmission of multidrug-resistant and toxigenic staphylococci.

Asymptomatic intramammary infection with multidrug-resistant gram-negative bacteria in a research dairy farm: incidence and genetic basis of resistance.

Nonpathogenic and opportunistic bacteria are increasingly recognized as reservoirs of antibiotic resistance genes. However, nothing is known about the mechanisms of antibiotic resistance in such bacteria isolated from the udders of healthy animals. In this study, 150 Gram-negative strains isolated from milk samples of healthy dairy cows were screened for the presence of a large pool of antibiotic resistance markers. Strains carrying ß-lactamase-resistance genes, including SHV-1, SHV-11, SHV-27, TEM-1, OXY-1, CTX-M-2 and class 1 integrons, were detected. Our findings give the first evidence that nonpathogenic and opportunistic bacteria carrying antibiotic resistance genes can asymptomatically invade healthy udders and suggest that they may play a role in the dissemination of antibiotic resistance genes to the other udder pathogens.

Prevalence and molecular characterization of ampicillin-resistant Enterobacteriaceae isolated from traditional Egyptian Domiati cheese.

The aim of this study was to address the prevalence and the molecular characteristics of antibiotic-resistant enteric bacteria isolated from one of the most popular types of Egyptian cheese. A total of 215 ampicillin-resistant enterobacterial isolates were obtained from 80 samples of Domiati cheese, and they were screened by PCR for a large pool of antibiotic resistance markers, including extended-spectrum beta-lactamases (ESBLs), class 1 and class 2 integrons, and plasmid-mediated quinolone resistance genes. It was determined that the most frequent mechanism of ampicillin resistance was from a TEM-1-type beta-lactamase. As well, SHV beta-lactamases, including SHV-1, SHV-25, and SHV-26, showed a high prevalence, and two novel SHV beta-lactamases, SHV-110 and SHV-111, were identified. Type CTX-M-14, OXY-1, OXA-1, and CMY-4 beta-lactamases were also detected in a few isolates. In addition, a novel AmpC beta-lactamase was detected that was designated CMY-41. Sequencing results of class 1 integrons revealed that the uncommon aminoglycoside resistance gene cassette aadA22 was found for the first time in an Escherichia coli strain. The other class 1 integrons harbored various common gene cassettes, including aadA1, aadA1a, aadA2, aadA12, dfr5, dfr7, dfr12, and dfr15. The only isolate that carried a class 2 integron contained dfrA1, sat2, and aadA1. Plasmid-mediated quinolone resistance determinants qnrS and qnrB showed a low prevalence. This study provides meaningful data on high antimicrobial resistance contained in Domiati cheese samples and reports for the first time the presence of beta-lactamases, plasmid-mediated quinolone resistance, and integrons in isolates from food of Egyptian animal origin.

First characterization and emergence of SHV-60 in raw milk of a healthy cow in Japan.

During monitoring of raw milk samples from healthy cows for the presence of antibiotic resistant bacteria, one isolate of Klebsiella pneumoniae strain HUF-100 was found to be resistant to oxyimino-cephalosporins and aztreonam. It was found to carry a chromosomally-encoded extended-spectrum beta-lactamase that has not been described previously, namely SHV-60. Thus, it must be expected that this strain will spread further among food-producing animals and thereby constitute a reservoir of this resistant strain and resistance gene that can transfer to and cause treatment problems for humans. The present study confirms the hypothesis that some of novel multiple antibiotic resistant zoonotic bacterial pathogens may initially emerge from food animals and reports, for the first time, this type of emergence in Japan.