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Obeng A.S.,University of South Australia | Rickard H.,University of South Australia | Sexton M.,Biosecurity SA | Pang Y.,Guangxi Veterinary Research Institute | And 2 more authors.
Journal of Applied Microbiology | Year: 2012

Aims: To evaluate the phenotypic and genotypic profiles of Campylobacter spp. from poultry faecal samples from free range or intensively raised meat chickens and free range egg layers. In addition, a case-comparison study of antibiotic resistance genes from different groups of poultry and some pig strains previously collected was carried out. Methods: Resistance to different antibiotics was assessed using the agar dilution method. In addition, all the strains were tested for ampicillin (blaOXA-61), erythromycin (aph-3-1), tetracycline tet(O), streptomycin (aadE), and the energy-dependent multi-drug efflux pump (cmeB) resistance genes using multiplex polymerase chain reaction. Results: The evaluation of phenotypic resistance revealed all of the strains from poultry were sensitive to ciprofloxacin, gentamicin, erythromycin or tylosin. But, widespread resistance to lincomycin (51-100%), extensive resistance to ampicillin (33·3-60·2%) and less resistance to tetracycline (5·6-40·7%) were observed in the different groups of chickens. Antibiotic resistance genes blaOXA-61, cmeB and tet(O) were found in 82·6-92·7%, 80·3-89% and 22·3-30·9% Camp. coli isolates from pigs, whilst 59-65·4% and 19·2-40·7% Camp. jejuni from chickens were found to encode blaOXA-61 and tet(O), respectively. Conclusion: No significant difference between isolates from free range egg layers and meat chickens (P < 0·05) was found. However, there were significant differences between the pig strains and all the groups of poultry strains (P < 0·05) with regard to carriage of resistance genes. In addition, pulsed field gel electrophoresis of selected resistant isolates from the poultry and pig revealed closely related clonal groups. Significance and Impact of the study: Our results suggest the resistant strains are persisting environmental isolates that have been acquired by the different livestock species. Furthermore, the different treatment practices in poultry and pigs have resulted in differences in resistance profiles in Campylobacter isolates. © 2012 The Society for Applied Microbiology. Source


Obeng A.S.,University of South Australia | Rickard H.,University of South Australia | Ndi O.,University of South Australia | Sexton M.,Biosecurity SA | Barton M.,University of South Australia
International Journal of Poultry Science | Year: 2014

Avian Pathogenic Escherichia coli (APEC) and some enterococci are important zoonotic pathogens associated with poultry and some human illnesses. This study was conducted to evaluate the phenotypic antibiotic resistance and resistance genes during the production cycle of healthy free-range meat chickens and egg layer pullets raised in two different controlled farms in South Australia, in particular to determine at which point in the production cycle birds become colonized with antibiotic resistant bacteria. Antibiotic resistance was investigated in faecal E. coli (206) and enterococcal (252) isolates by agar dilution and polymerase chain reaction. Southern hybridization was carried on plasmids from selected multi-resistant E. coli isolates to determine the location of resistance genes. Our results revealed that birds are colonized with resistant bacteria encoding various resistance genes from a very early age. Resistance to ampicillin and tetracycline (and associated resistance genes) were the most frequently detected resistances in E. coli isolates from egg layer pullets and free-range meat chickens. Phenotypically resistant enterococcal isolates from 3-5 days old chickens carried genetic determinants for resistance to tetracycline, bacitracin and tylosin. Whilst statistical analysis revealed there was no significant differences (p<0.05) with the phenotypic resistance observed in the E. coli and enterococcal isolates from meat chickens and egg layer pullets, a significant difference was observed in resistant E. coli isolates containing blaTEM and tet genes. This study demonstrates that newly hatched chicks are already colonized with resistant bacteria which persist through the production cycle and can potentially contaminate eggs and chicken carcasses. This study also confirms that poultry are a potential source of pathogenic E. coli strains. © Asian Network for Scientific Information, 2014. Source


Obeng A.S.,University of South Australia | Rickard H.,University of South Australia | Ndi O.,University of South Australia | Sexton M.,Biosecurity SA | Barton M.,University of South Australia
Avian Pathology | Year: 2013

Resistance to antimicrobials in enterococci from poultry has been found throughout the world and is generally recognized as associated with antimicrobial use. This study was conducted to evaluate the phenotypic and genotypic profile of enterococcal isolates of intensive (indoor) and free range chickens from 2008/09 and 2000 in order to determine the patterns of antimicrobial resistance associated with different management systems. The minimum inhibitory concentrations in faecal enterococci isolates were determined by agar dilution. Resistance to bacitracin, ceftiofur, erythromycin, lincomycin, tylosin and tetracycline was more common among meat chickens (free range and intensive) than free range egg layers (P<0.05). Isolates were evaluated by polymerase chain reaction for bacitracin (bcrR), tylosin (ermB), tetracycline (tet(L), tet(M), tet(O), tet(S), and tet(K)), gentamicin (aac6-aph2), vancomycin (vanC and vanC2), ampicillin (pbp5) and integrase (int) genes. Resistance to bacitracin, erythromycin and tetracycline were found to be correlated with the presence of bcrR, ermB, and tet genes in most of the isolates collected from meat chickens. Most bacteria encoding ermB gene were found to express cross-resistance to erythromycin, tylosin and lincomycin. No significant difference was found in these resistance genes between isolates sampled in 2000 and 2008/09 (P<0.5). Unlike the enterococcal strains sampled in 2000, the 2008/09 isolates were found to be susceptible to vancomycin and virginiamycin. This study provides evidence that, despite strict regulation imposed on antibiotic usage in poultry farming in Australia, antimicrobial resistance is present in intensively raised and free range meat chickens. © 2013 Copyright Houghton Trust Ltd. Source


Mutze G.,Biosecurity SA | Cooke B.,University of Canberra | Lethbridge M.,Flinders University | Jennings S.,Water and Natural Resources
Rangeland Journal | Year: 2014

European rabbits are severe environmental pests in Australia but reporting of density-damage relationships has been hindered by a lack of simple methods to estimate the density of rabbit populations in native vegetation. A methodology for quantifying rabbit densities suitable for use in sparse populations of rabbits in conjunction with surveys of the condition of native vegetation is proposed. Dung pellets were counted in 11629 regularly-spaced quadrats of 0.1m2 in semiarid, coastal and cool-temperate areas of southern Australia. Mean pellet counts in latrines and the relationship between dung counts outside of latrines and the proportion of quadrats falling on latrines were quantified. This allowed density of dung pellets to be estimated by using a correction factor for latrines instead of attempting to count all pellets within quadrats that included parts of latrines. Rabbit density was calculated from pellet density based on mean pellet size, pellet breakdown rate and estimates of rabbits' dry matter intake and digestive efficiency. Results were validated against estimates of rabbit density from long-term studies using a combination of spotlight transect counts and burrow entrance counts. The proposed methodology allows estimates of rabbit density in native vegetation to be obtained from just a few hours work and can be used in conjunction with surveys of the condition of native vegetation to quantify rabbit impacts. This methodology is seen as particularly useful in providing a tool to allow rabbit densities to be estimated and then compared with the thresholds, determined separately, at which damage occurs for given ecosystems. © Australian Rangeland Society 2014. Source


News Article
Site: http://www.biosciencetechnology.com/rss-feeds/all/rss.xml/all

An American company that bills itself as a pioneer in tracking emerging epidemics made a series of costly mistakes during the 2014 Ebola outbreak that swept across West Africa - with employees feuding with fellow responders, contributing to misdiagnosed Ebola cases and repeatedly misreading the trajectory of the virus, an Associated Press investigation has found. San Francisco-based Metabiota Inc. was tapped by the Sierra Leonean government and the World Health Organization to help monitor the spread of the virus and support the response after Ebola was discovered circulating in neighboring Guinea in March 2014. But emails obtained by AP and interviews with aid workers on the ground show that some of the company's actions made an already chaotic situation worse. WHO outbreak expert Dr. Eric Bertherat wrote to colleagues in a July 17, 2014, email about misdiagnoses and "total confusion" at the Sierra Leone government lab Metabiota shared with Tulane University in the city of Kenema. He said there was "no tracking of the samples" and "absolutely no control on what is being done." "This is a situation that WHO can no longer endorse," he wrote. Metabiota chief executive officer and founder Nathan Wolfe said there was no evidence his company was responsible for the lab blunders, that the reported squabbles were overblown and that any predictions made by his employees didn't reflect the company's position. He said Metabiota doesn't specialize in outbreak response and that his employees stepped in to help and performed admirably amid the carnage of the world's biggest-ever Ebola outbreak. "Metabiota's team worked tirelessly, skillfully and at substantial potential danger to themselves to assist when most of the world was still ignoring the problem," he said in an email. "We are proud of our team efforts which went above and beyond the call of duty." Wolfe said some of the problems flagged were misunderstandings - and that others were planted by commercial rivals. The complaints about Metabiota mirror the wider mismanagement that hamstrung the world's response to Ebola, a disease that has killed upward of 11,000 people. Previous AP reporting has shown that WHO resisted sounding the alarm over Ebola for two months on political, religious and economic grounds and failed to put together a decisive response even after the alert was issued. The turmoil that followed left health workers in Kenema bereft of protective equipment or even body bags and using expired chlorine, a crucial disinfectant. WHO said Metabiota was well-placed to help when Ebola broke out in West Africa because of its expertise with Lassa, a related disease. The agency declined to give any detail about how it dealt with the complaints from senior staff about the firm or the status of their current relationship. In Sierra Leone, Sylvia Blyden, who served as special executive assistant to the country's president in the early days of the outbreak, said Metabiota's response was a disaster. "They messed up the entire region," she said. She called Metabiota's attempt to claim credit for its Ebola work "an insult for the memories of thousands of Africans who have died." Wolfe, a swashbuckling scientist sometimes described as the Indiana Jones of virology, has focused his company's work on disease hotspots like West Africa in a bid to sniff out the next big threat. In his book, "The Viral Storm," Wolfe writes that his work is aimed at hunting down "the first moments at the birth of a new pandemic" to prevent its global spread. With a doctorate in immunology and infectious diseases from Harvard, Wolfe, 45, has found some serious backers. Metabiota and its nonprofit sister company Global Viral have received millions in funding from USAID, Google and the Skoll Foundation, among others. The Department of Defense alone has granted more than $18 million worth of contracts to the firm, federal records show. In the early months of the outbreak, with WHO and the Centers for Disease Control and Prevention thin on the ground, Metabiota said it stepped in to help at the request of the Sierra Leonean government. An account posted to its website says Metabiota provided "critical support" in the earliest days of the outbreak, organizing training, jointly running Sierra Leone's Ebola laboratory, assisting with outbreak logistics and producing daily reports for the government. Messages saved to ProMed, a mailing list for outbreak watchers, are upbeat, describing Metabiota's tests and how it was teaching Sierra Leoneans how to set up Ebola isolation wards. On May 12, senior Metabiota scientist Dr. Jean-Paul Gonzalez said preparedness work had "ultimately protected, or at least uniquely prepared, Sierra Leone." But there were already reports of suspected infections in the country and, within weeks, the virus tore through Sierra Leone, overwhelming the hospital in Kenema where Metabiota shared the 700-square-foot (65-square-meter) lab with Tulane. To some at Tulane, which had a long-established research project at the lab, Metabiota's missteps were predictable. The two groups worked side-by-side in an uneasy relationship that observers said sometimes tipped into open conflict. Tulane microbiology professor Bob Garry questioned whether Gonzalez was the right person to teach Sierra Leoneans how to protect themselves from Ebola. In 1994, the French researcher was at the center of a safety scare at Yale University after he accidentally infected himself with the rare Sabia virus and didn't notify officials there for more than a week. The university put more than 100 people under surveillance and ordered Gonzalez to take a remedial safety course. Garry said that should have raised a red flag. "Do you really want the person who infected himself with hemorrhagic fever going around explaining to people how to be safe?" he asked. Gonzalez referred questions to a Metabiota press representative, who said in an email that the incident happened more than 20 years ago and that Gonzalez has extensive lab safety experience. But Garry also faced questions; the WHO emails obtained by AP complaining about the Kenema lab are as critical of Tulane as they are of Metabiota. Garry acknowledged mistakes but said they were understandable given the chaotic circumstances. "We didn't have the personnel and the infrastructure that was needed to handle the onslaught of cases that were coming," he said. "We were doing the best we had with what we had there." "THEY WERE AT WAR" As the death toll mounted in July, scientists from WHO, the United States and Canada were voicing concerns about what Metabiota and its Tulane colleagues were doing at the Kenema lab, according to the emails obtained by AP and interviews with those on the ground at the time. When Gary Kobinger, head of special pathogens at the Public Health Agency of Canada, double-checked some of the facility's work in mid-July, he found worrying discrepancies in four of eight tests and identified up to five people wrongly diagnosed with Ebola, among them a worker with the medical charity Doctors Without Borders. Kobinger told AP in a telephone interview that the misdiagnoses he caught suggested many more had gone unnoticed. "If you detect two, three, four, five, how many are out there?" he said. The mistakes were doubly dangerous in a country where many mistrusted international workers, who were suspected of spreading Ebola deliberately, said Bertherat, the WHO outbreak expert. Attempts to reassure a jittery public could be "totally ruined if the population does not trust anymore in the diagnostic of the medical teams," he wrote in an email. Bertherat proposed two fixes for the problematic lab: WHO could either train Metabiota and Tulane staffers, or close down the facility and transfer all testing to another lab. He told his boss on July 18, 2014, that shutting down the shared lab was the "more prudent" option. Five days later, Geneva-based WHO staffer Pat Drury emailed the agency's chief, Dr. Margaret Chan, with criticism of both Tulane and Metabiota, referring to their shared facility as two labs. "Both labs do not meet international standards for Biosecurity," he said, adding that "several patients have been wrongly tested positive." Metabiota founder Wolfe said "we did wonderful lab work as far as I'm concerned." Errors in the shared facility stopped once "other groups" were pulled from the testing and, in any case, he noted that Metabiota tested over 1,800 samples. Even if any mistakes were made, he said the error rates were well within ranges seen elsewhere. Wolfe did not name the "other groups," but documents and interviews show Metabiota and Tulane blamed each other. "On the surface, they were collaborating," Kobinger said. But in reality, "they were at war." U.S. health official Austin Demby, who was sent to evaluate the lab's work at the request of the CDC and Sierra Leone, said initial diagnostic tests carried out by Metabiota and Tulane clashed as often as 30 percent of the time. Errors raised the risk that the virus could be spread further by sending infected patients home or confining otherwise healthy people to infectious Ebola wards. In a July 21 email to CDC and State Department officials, Demby put the blame at Tulane's door, saying Metabiota's tests were always closer to the mark and that Tulane's "add no real value to the diagnosis." But Tulane's Garry said Metabiota's staff stirred confusion by not following protocol. Wolfe said that was "simply false." The lab's set-up also was worrisome. Used needles littered the place, according to a worker who spoke on condition of anonymity because the worker was not authorized to speak to the media. Demby said in his email that the lab lacked an ultraviolet light for decontamination and didn't have enough space to process blood samples safely. "The cross contamination potential is huge and quite frankly unacceptable," he wrote. Tulane pulled the plug on its tests soon thereafter and the lab's results improved. Kobinger credited Metabiota researcher Nadia Wauquier - "the hero of that whole gang" - with tightening procedures, but eventually the company was relieved of its testing duties and the CDC took over. Both Tulane and Metabiota say they stepped aside voluntarily. Outside the lab, the training touted by Metabiota unnerved some fellow responders. Anja Wolz, an emergency coordinator with Doctors Without Borders, told AP in an interview that she saw Metabiota workers enter the homes of suspected Ebola patients without protective gear and without decontaminating themselves before leaving high-risk areas. "They didn't even have chlorine with them to wash their hands," she said, adding that Metabiota project coordinator James Bangura told her they didn't need the critical disinfectant. "I didn't go inside the Metabiota lab," she said. "I refused to go because I had already seen enough." Aid workers also complained that Metabiota employees including Bangura and a Ugandan consultant hijacked the outbreak response in Kenema, which was supposed to be directed by WHO. Metabiota staffers "are systematically obstructing any attempt to improve the existing surveillance system and there are a lot of improvement(s) needed," WHO Ebola coordinator Philippe Barboza said in an August 8, 2014, email. The next day, he argued that WHO should pull its outbreak staff from Kenema so they wouldn't be tarred with Metabiota's failures, writing he was "very concerned of the potential reputational risk for WHO." British disease expert Chris Lane echoed Barboza's concerns. In a message to Barboza, he lamented that "much good work was achieved prior to the arrival of the Metabiota field staff." Barboza and Lane declined comment on the arguments. Metabiota officials acknowledged the dispute but downplayed it. "It is inaccurate to suggest a major conflict between WHO and Metabiota," Wolfe said, noting that Bangura was awarded a Sierra Leonean presidential silver medal for his Ebola efforts. Nevertheless, the disagreement was serious enough that Metabiota said it fired the consultant and pulled Bangura from Kenema. The consequences went beyond office politics. In one email, Barboza said 1 million euros in funding proposed by the International Rescue Committee was being held up because the donors wanted "a clear WHO leadership." Some responders said one of the most disturbing mistakes Metabiota employees made was misreading the epidemic. Wolz, of Doctors Without Borders, said she recalled a meeting in the early summer as cases began multiplying "when I said that the outbreak was completely out of control." She said Metabiota responded, 'No, we know where we are, everything is OK.'" Kobinger, the Canadian scientist, said Bangura would interpret temporary dips in the number of cases to mean that the outbreak was dissipating. He said he couldn't fathom that reasoning given the number of Ebola-positive samples pouring into his own lab in nearby Kailahun. Though Bangura said he did not personally make any estimates, Kobinger said Bangura told him in July that the outbreak would be over in "two or three weeks." Any suggestion Metabiota wrongly forecast the Ebola epidemic is rejected by Wolfe, who once wrote that his career is focused on creating systems "that can accurately detect pandemics early, determine their likely importance, and, with any luck, crush those that have the potential to devastate us." Wolfe told AP that his company couldn't be held responsible for the predictions of employees seconded to Sierra Leone's Health Ministry. "We didn't make forecasts. We loaned individuals to the ministry," Wolfe said. "So the notion that somehow it's a Metabiota forecast is simply completely inaccurate." Fellow responders may not have grasped the distinction. On Aug. 11 - just three days after WHO had declared the crisis a global emergency - Metabiota employees presented a slideshow to an Ebola task force. Next to a bar chart showing a slowdown in cases were the words: "The outbreak is stabilizing." "This is the kind of report we get from Metabiota epidemiologists," she emailed colleagues from the presentation. "They are sending wrong messages. The outbreak is clearly not stabilizing." It was only in the second half of August that Kenema numbers began falling and, even then, the virus was merely moving to more populated areas. Nearly two years after the virus was first discovered circulating near its border, Sierra Leone still is not officially Ebola-free. "THEY MESSED UP ON EBOLA" Despite doubts about Metabiota's performance, Wolfe's firm has largely been congratulated on its work in West Africa. In December 2014, it won a European Union grant to help validate new tests and treatments for the disease, something a company official said was in recognition of "the critical contributions our team has made in supporting the current outbreak." In 2015, the company raised some $30 million in investment from four U.S. investment firms intended to "support Metabiota's efforts to further develop and deliver epidemic risk management worldwide," according to a press release. Even WHO has publicly credited Metabiota for its work during the outbreak. Months after Senga, one of its employees, complained privately about Metabiota's optimistic predictions in Kenema, she wrote a sunnier account on WHO's website. "The fact that they were already there helped a lot," she wrote in a post called "Ebola Diaries." Tulane and Metabiota employees already being established in Kenema "made our case investigations and contact tracing work a lot easier," she wrote. Guillaume Lachenal, a medical historian at Paris Diderot University who has followed Metabiota's work in Africa, said it was indecent of the company to claim Ebola as a success story. "They messed up on Ebola. That can happen," he said. "To make a success story out of their Ebola response, that's quite something." Satter and Cheng also reported from London. Krista Larson contributed to this report from Kenema, Sierra Leone. Lisa Leff contributed from San Francisco.

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