National Antimicrobial Resistance Research Articles

Antimicrobial resistance in the WHO African region: current status and roadmap for action.

The high burden of communicable diseases in African countries engenders extensive antimicrobial use and subsequent resistance with substantial health, financial and societal implications. A desktop analysis to ascertain whether countries in the WHO African region have implemented the WHO Policy Package to combat antimicrobial resistance (AMR) revealed that just two countries (4.3%) have national AMR plans in place, 14.9% (7) have overarching national infection prevention and control (IPC) policies, 93.6% (44) have essential medicines lists and 91.5% (43) have national medicines policies and treatment guidelines intimating rational use. None currently have representative national surveillance systems nor do any incentivize research and development into new medicines and diagnostics. A regional situational analysis to identify scalable good practices within African, resource-constrained country contexts under the auspices of WHO-AFRO is a necessary initial step towards the development of national and regional action plans in concert with incremental progress towards achieving the objectives of the policy package and global action plan. While it is clearly the responsibility of governments to develop, resource and implement plans, regular reporting to and/or monitoring and evaluation by an overarching body such as WHO-AFRO will ensure persistent incremental progress within continuous quality and accountability improvement paradigms.

Antibiotic Resistance Patterns of Major Zoonotic Pathogens from All-Natural, Antibiotic-Free, Pasture-Raised Broiler Flocks in the Southeastern United States.

The use of antibiotics in agroecosystems has been implicated in the rise in antibiotic resistance (AR), which can affect environmental, animal, and human health. To determine the environmental impact of antibiotic use in agroecosystems, appropriate background levels of AR in agricultural environments in the absence of antibiotic application must be determined. Therefore, to determine background levels of AR in broiler production, four target microbes (, , , and ) were isolated from 15 all-natural, antibiotic-free, pasture-raised broiler flocks from six farms within the southeastern United States. The AR profiles of these isolates were characterized using the CDC National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS), and these resistance patterns were compared across target microbes and farms and throughout the life cycle of the flocks along the farm-to-fork continuum. Antibiotic resistances were most prevalent in and and least prevalent in . Although and were isolated from the same farms and characterized using the same NARMS plates, they exhibited distinct AR profiles, with demonstrating clear farm-specific resistance patterns. Multidrug resistance rates (three or more antibiotics), in order of prevalence, were (63.9%), (36.0%), (12.7%), and (1.4%). The results of this study demonstrate the variability in background AR among major food safety-related microbes, even when isolated from similar production and processing samples from the same farms, and indicate the need for the proper design of future broiler production studies to account for this highly dynamic background AR.

Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli.

For Enterobacteriaceae such as Salmonella spp. and Escherichia coli, no unified interpretive resistance criteria exist for streptomycin, an epidemiologically important antibiotic. As part of the National Antimicrobial Resistance Monitoring System, we had previously used a minimum inhibitory concentration of ≥ 64 μg mL(-1) as an epidemiological cutoff value (ECV) to define non-wild-type isolates. To identify whether this ECV correlated with genetic determinants of resistance, we performed whole-genome sequencing of 463 Salmonella and E. coli isolates to identify streptomycin resistance genotypes. From this analysis, we found that using a streptomycin resistance breakpoint of ≥ 64 μg mL(-1) classified over 20% of strains possessing aadA or strA/strB resistance genes as wild-type. Therefore, to improve the concordance between genotypic and phenotypic data, we propose reducing the phenotypic cutoff values to ≥ 32 μg mL(-1) for both Salmonella and E. coli, to be used widely as ECVs to categorize non-wild-type isolates.

Estimated Incidence of Antimicrobial Drug-Resistant Nontyphoidal Salmonella Infections, United States, 2004-2012.

Salmonella infections are a major cause of illness in the United States. The antimicrobial agents used to treat severe infections include ceftriaxone, ciprofloxacin, and ampicillin. Antimicrobial drug resistance has been associated with adverse clinical outcomes. To estimate the incidence of resistant culture-confirmed nontyphoidal Salmonella infections, we used Bayesian hierarchical models of 2004–2012 data from the Centers for Disease Control and Prevention National Antimicrobial Resistance Monitoring System and Laboratory-based Enteric Disease Surveillance. We based 3 mutually exclusive resistance categories on susceptibility testing: ceftriaxone and ampicillin resistant, ciprofloxacin nonsusceptible but ceftriaxone susceptible, and ampicillin resistant but ceftriaxone and ciprofloxacin susceptible. We estimated the overall incidence of resistant infections as 1.07/100,000 person-years for ampicillin-only resistance, 0.51/100,000 person-years for ceftriaxone and ampicillin resistance, and 0.35/100,000 person-years for ciprofloxacin nonsusceptibility, or ≈6,200 resistant culture-confirmed infections annually. These national estimates help define the magnitude of the resistance problem so that control measures can be appropriately targeted.

Comparison of mixed effects models of antimicrobial resistance metrics of livestock and poultry Salmonella isolates from a national monitoring system

Antimicrobial use in agriculture is considered a pathway for the selection and dissemination of resistance determinants among animal and human populations. From 1997 through 2003 the U.S. National Antimicrobial Resistance Monitoring System (NARMS) tested clinical Salmonella isolates from multiple animal and environmental sources throughout the United States for resistance to panels of 16–19 antimicrobials. In this study we applied two mixed effects models, the generalized linear mixed model (GLMM) and accelerated failure time frailty (AFT-frailty) model, to susceptible/resistant and interval-censored minimum inhibitory concentration (MIC) metrics, respectively, from Salmonella enterica subspecies enterica serovar Typhimurium isolates from livestock and poultry. Objectives were to compare characteristics of the two models and to examine the effects of time, species, and multidrug resistance (MDR) on the resistance of isolates to individual antimicrobials, as revealed by the models. Fixed effects were year of sample collection, isolate source species and MDR indicators; laboratory study site was included as a random effect. MDR indicators were significant for every antimicrobial and were dominant effects in multivariable models. Temporal trends and source species influences varied by antimicrobial. In GLMMs, the intra-class correlation coefficient ranged up to 0.8, indicating that the proportion of variance accounted for by laboratory study site could be high. AFT models tended to be more sensitive, detecting more curvilinear temporal trends and species differences; however, high levels of left- or right-censoring made some models unstable and results uninterpretable. Results from GLMMs may be biased by cutoff criteria used to collapse MIC data into binary categories, and may miss signaling important trends or shifts if the series of antibiotic dilutions tested does not span a resistance threshold. Our findings demonstrate the challenges of measuring the AMR ecosystem and the complexity of interacting factors, and have implications for future monitoring. We include suggestions for future data collection and analyses, including alternative modeling approaches.

Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2')-If, aph(2″)-Ig, aph(2″)-Ih, aac(6')-Ie-aph(2″)-Ia, aac(6')-Ie-aph(2″)-If, aac(6')-Im, aadE, sat4, ant(6'), aad9, aph(3')-Ic, and aph(3')-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs.

Antimicrobial Stewardship in Australian Hospitals and Other Settings.

Australia’s model of antimicrobial stewardship (AMS) has evolved significantly over recent years, from a long-standing national approach of antimicrobial prescribing guidelines and antimicrobial prescribing restrictions to recent advances including the first National Antimicrobial Resistance Strategy and incorporating mandatory AMS as part of hospital accreditation standards. AMS programs are most commonly found in the hospital setting. Various models are used throughout the country based on the local context and resources available. Programs implemented at Alfred Health and the Royal Brisbane and Women’s Hospital represent two successful models in tertiary referral settings that accommodate a general ward setting as well as specialized areas with a high infection burden. Measurement of outcomes related to AMS activities remains poorly standardized, with process indicators such as antimicrobial utilization forming a large proportion of outcome measurement. Presently there is no requirement for any AMS outcome measurements to be reported externally. Point prevalence surveys of appropriateness of prescribing and compliance with prescribing guidelines are widely used at a national level. Despite this, there is still a paucity of published Australian data to support the effect of AMS on patient clinical outcomes. Private hospitals, the community, veterinary medicine and aged care sectors represent an important area for future AMS expansion within Australia. The AMS focus has traditionally been on prescribing restrictions (through the Commonwealth funding agencies); however, recent work has described other areas for improvement and development in both settings. AMS in Australia continues to evolve. The recent development of an Australian strategic plan to link antimicrobial utilization and resistance surveillance with policy represents an important step forward for the future of AMS in Australia.

Narrative review of primary care point-of-care testing (POCT) and antibacterial use in respiratory tract infection (RTI)

Antimicrobial resistance is a global problem and is being addressed through national strategies to improve diagnostics, develop new antimicrobials and promote antimicrobial stewardship. A narrative review of the literature was...

Performance evaluation of the microbiology laboratories in Turkey for culture and antibiotic susceptibility tests and the selection of laboratories to provide data for National Antimicrobial Resistance Surveillance System: Questionnary application

Performance evaluation of the microbiology laboratories in Turkey for culture and antibiotic susceptibility tests and the selection of laboratories to provide data for National Antimicrobial Resistance Surveillance System: Questionnary application

Public Health England 2013 Annual Conference: highlights and looking ahead.

Overview - Anthony Kessel and Emmeline BuckleyThe historian Dorothy Porter has described public health as collective action in relation to the health of populations. This definition de-emphasizes the contributions of professionals or particular interest groups, and instead stresses the essential collaborative nature of public health work. The sentiment of Porter's definition was at the heart of the 2013 Public Health England (PHE) Annual Conference.Held on 10 - 11th September 2013, this was the inaugural conference for PHE, the new national public health organization. As such, the meeting was oriented towards bringing together a range of partners and stakeholders from the diverse public health landscape of this country, and providing a forum to galvanize the new public health system.Over 1300 delegates attended the conference, including representatives from PHE, local authorities, NHS, universities, the voluntary sector, government departments and the many other organizations and groups that work collectively in relation to population and community health. Around 30 delegates from over 15 countries overseas were warmly welcomed. Over the two days the programme included over 40 sessions covering areas such as sexual health, social determinants, population healthcare, global health, transport and local government, unemployment and health inequalities, emerging diseases, the national vaccination programme, mental health and antimicrobial resistance. There were also more than 300 posters on display.In this edition of Perspectives we have the opportunity to present a series of brief snapshots of the days' events. The articles cover a wide range of issues including: the progress of an intervention to reduce teenage pregnancy in Hull; developing capacity in the field epidemiology workforce; and assessing environmental chemical exposures. Also included is the write-up of an award-winning poster, describing a partnership approach to preventing excess winter deaths in Lancashire.3 These papers go some way towards showcasing the breadth of expertise on display at the conference. Further examples of the work presented at the PHE conference can be found in the Royal Society for Public Health's sister journal, Public Health.Overall, the conference managed to display the strength of talent amongst those involved in public health in this country, and also exemplified the immense importance of collaboration with partners across sectors in the UK and internationally. The conference set a benchmark in terms of scientific quality as well as practical significance for public health delivery, and has provided a platform on which the second PHE conference in 2014 can build.Improving the health and wellbeing of adolescents: what can we learn from Europe and apply locally? - Ann Hoskins and Fiona BrooksThere are 7.4 million adolescents aged 10-19 living in the UK, representing 12% of the total UK population - the same proportion as the over-70s age group.1 Although considerable gains over the latter half the twentieth century have been made in terms of reductions in infant mortality and increased life expectancy for older people, adolescents have experienced relatively less improvement in their health and well-being than other age groups.2The second decade of life marks an important phase in the life course; not only do young people have to traverse important physical and developmental milestones, but they also gain greater autonomy and control over decision- making relating to health and health behaviours. Health-related behaviours established in adolescence, such as tobacco use, alcohol consumption and dietary habits and physical activity, may influence future health, with implications for long term conditions, health complaints and emotional well- being and mental health.The current generation of children entering adolescence and early adulthood also face considerable new challenges, including increasing academic expectations and uncertainties about future employment as well as changing social relationships (increasingly influenced by the presence of social media and the virtual world). …

Quinolone-resistant Salmonella enterica serotype Enteritidis infections associated with international travel.

We found a strong association between nalidixic acid-resistant Salmonella enterica serotype Enteritidis infections in the United States and recent international travel by linking Salmonella Enteritidis data from the National Antimicrobial Resistance Monitoring System and the Foodborne Diseases Active Surveillance Network.

Clinical Outcomes of Nalidixic Acid, Ceftriaxone, and Multidrug-Resistant Nontyphoidal Salmonella Infections Compared with Pansusceptible Infections in FoodNet Sites, 2006–2008

Nontyphoidal Salmonella causes an estimated 1.2 million infections, 23,000 hospitalizations, and 450 deaths annually in the United States. Most illnesses are self-limited; however, treatment with antimicrobial agents can be life-saving for invasive infections. The Foodborne Diseases Active Surveillance Network and the National Antimicrobial Resistance Monitoring System collaborated on a prospective cohort study of patients with nontyphoidal Salmonella bloodstream and gastrointestinal infections to determine differences in the clinical outcomes of resistant compared with pansusceptible infections. Interviews were conducted within 85 days of specimen collection date. Of 875 nontyphoidal Salmonella isolates, 705 (81%) were pansusceptible, 165 (19%) were resistant to at least 1 agent, and 5 (0.6%) had only intermediate resistance. The most common pattern, found in 51 (31%) of resistant isolates, was resistance to at least ampicillin, chloramphenicol, streptomycin, sulfisoxazole, and tetracycline (ACSSuT); 88% of isolates with this pattern were serotype Typhimurium or Newport. Fourteen (52%) of the 27 ceftriaxone-resistant isolates were also ACSSuT resistant. Adjusted for age and serotype, bloodstream infection was significantly more common among patients infected with strains resistant to only two, only three, or only five antimicrobial classes, to ACSSuT with or without other agents, to ACSSuT only, or to nalidixic acid with or without other agents than among patients with pansusceptible isolates. Adjusted for age, serotype, and bloodstream infection, hospitalization was significantly more common among patients infected with strains resistant to only three agents or to ceftriaxone (all ceftriaxone-resistant isolates were resistant to other agents) than among patients with pansusceptible isolates. This study extends evidence that patients with antimicrobial-resistant nontyphoidal Salmonella infections have more severe outcomes. Prevention efforts are needed to reduce unnecessary antimicrobial use in patient care settings and in food animals to help prevent the emergence of resistance and infections with resistant nontyphoidal Salmonella.

Characterization ofblaCMYPlasmids and Their Possible Role in Source Attribution ofSalmonella entericaSerotype Typhimurium Infections

Salmonella is an important cause of foodborne illness; however, identifying the source of these infections can be difficult. This is especially true for Salmonella serotype Typhimurium, which is found in diverse agricultural niches. Extended-spectrum cephalosporins (ESC) are one of the primary treatment choices for complicated Salmonella infections. In Salmonella, ESC resistance in the United States is mainly mediated by blaCMY genes carried on various plasmids. In this study, we examined whether the characterization of blaCMY plasmids, along with additional information, can help us identify potential sources of infection by Salmonella, and used serotype Typhimurium as a model. In the United States, monitoring of retail meat, food animals, and ill persons for antimicrobial-resistant Salmonella is conducted by the National Antimicrobial Resistance Monitoring System. In 2008, 70 isolates (70/581; 12.0%) (34 isolates from retail meat, 23 food animal, and 13 human) were resistant to ceftriaxone and amoxicillin/clavulanic acid. All were polymerase chain reaction (PCR)-positive for blaCMY and 59/70 (84.3%) of these genes were plasmid encoded. PCR-based replicon typing identified 42/59 (71.2%) IncI1-blaCMY plasmids and 17/59 (28.8%) IncA/C-blaCMY plasmids. Isolates from chickens or chicken products with blaCMY plasmids primarily had IncI1-blaCMY plasmids (37/40; 92.5%), while all isolates from cattle had IncA/C-blaCMY plasmids. Isolates from humans had either IncA/C- blaCMY (n=8/12; [66.7%]) or IncI1- blaCMY (n=4/12 [33.3%]) plasmids. All of the IncI1-blaCMY plasmids were ST12 or were closely related to ST12. Antimicrobial susceptibility patterns (AST) and pulsed-field gel electrophoresis (PFGE) patterns of the isolates were also compared and differences were identified between isolate sources. When the source of a Typhimurium outbreak or sporadic illness is unknown, characterizing the outbreak isolate's blaCMY plasmids, AST, and PFGE patterns may help identify it.

Aetiological profile and antibiotic susceptibility pattern in patients with urinary tract infection in tripura.

Aetiological profile and antibiotic susceptibility pattern in patients with urinary tract infection in tripura.

Improvement plan for the korean nationwide surveillance of antimicrobial resistance program.

In recent years, the sudden increase in the prevalence of antimicrobial-resistant bacteria and the emergence of multidrug-resistant bacteria have become serious worldwide problems. Therefore, in 2000, the World Health Organization (WHO) declared antimicrobial resistance to be an international danger, and has been working with its member nations to promote the appropriate use of antimicrobials as a solution to the antimicrobial resistance threat [1]. The recent emergence of New Delhi metallo-β-lactamase carbapenem-resistant Enterobacteriaceae has motivated us to increase our alertness to antimicrobial-resistant organisms [2]. Thus, surveillance of healthcare-associated infection has been enhanced. Surveillance for antimicrobial resistance is being executed mainly in European countries and in the U.S. In Korea, with the enactment of the Infectious Disease Control and Prevention Act in December 2010, infectious diseases caused by 6 types of multidrug-resistant bacteria-vancomycin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus, methicillin-resistant S. aureus, multidrug-resistant Pseudomonas aeruginosa, multidrug-resistant Acinetobacter baumannii, and carbapenem-resistant Enterobacteriaceae-were legally designated for sentinel surveillance [3]. The prevalence of antimicrobial resistance in bacteria varies substantially from country to country and according to the date of the analysis and the hospital characteristics, because it is influenced significantly by the use of antimicrobial drugs and the degree of success of efforts to control the spread of resistant bacteria. The purposes of an antimicrobial resistance surveillance system (ARSS) are as follows: (1) to detect antimicrobial susceptibility patterns; (2) to monitor the identity, transmission, and expression of antimicrobial-resistance genes; (3) to provide important information on the development of bacterial resistance mechanisms in different regions; and (4) to allow changes in antimicrobial prescription practices and participation of infection control professionals. Well-designed antimicrobial resistance surveillance systems are needed when fighting bacterial resistance. The parameters of an ideal ARSS are as follows: global geography, year-on-year longevity, multiple species selection, centralized methods and test sites, large sample size, monitoring for many antimicrobial drugs, incorporation of epidemiology, and frequent data distribution [4]. Implementation of an ARSS requires 4 components: administrative commitments, system organization (participant, expert, and coordinator), financial support (from government agencies and the pharmaceutical industry), and data analysis and reporting systems (online and offline). The scope of ARSS networks is divided into global, continental, and nationwide. The global representative ARSSs are the Alexander Project, MYSTIC Program, SENTRY Program, PROTEKT System, and WHO Program. The European ARSS (EARSS; EARS-Net) is the surveillance system implemented in Europe, and the ARSSs available in the U.S. are the National Nosocomial Infections Surveillance, Intensive Care Antimicrobial Resistance Epidemiology, National Antimicrobial Resistance Monitoring System, International Surveillance Program for Emerging Antimicrobial Resistance, and Surveillance for Emerging Antimicrobial Resistance Connected to healthcare. In Korea, the nationwide ARSSs are the Korean Nationwide Surveillance of Antimicrobial Resistance (KONSAR), Korean Nosocomial Infections Surveillance System, and Korean Antimicrobial Resistance Monitoring System. Since 1997, the KONSAR program has been collecting data on antimicrobial-resistant bacteria from participating laboratories [5], and has therefore played an integral role in informing interested parties about the current state and severity of domestic antimicrobial resistance in bacteria by analyzing and reporting bacterial antimicrobial susceptibility data. However, the KONSAR program releases all its laboratory data to research papers or newsletters only after analysis; therefore, a web-based system that can analyze data in real time is needed [6]. To create such a system, a knowledge-based rule check system capable of detecting errors by setting the exact data variables as the definition of the specimen, the species identification method, and the antimicrobial susceptibility test methods must be defined. Furthermore, various analysis functions such as data comparison between entire hospitals and participating laboratories, and between peer groups, must be made possible on the internet. According to a recent KONSAR report [7], susceptibility to antimicrobials, including colistin, was analyzed without dividing Acinetobacter spp. into A. baumannii and non-baumannii Acinetobacter. This is a problem that has yet to be resolved. At the government level, blaOXA-23-like or ISAba1-activated blaOXA-51-like gene tests for detecting carbapenem-resistant A. baumannii need to be supported. For manufacturers that supply identification kits and for clinical microbiology laboratories, the development of testing methods that can accurately identify A. baumannii is also needed.

Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5− Strain Isolated from Chicken Breast

Salmonella enterica subsp. enterica serovar Typhimurium is a leading cause of salmonellosis. Here, we report a closed genome sequence, including sequences of 3 plasmids, of Salmonella serovar Typhimurium var. 5− CFSAN001921 (National Antimicrobial Resistance Monitoring System [NARMS] strain ID N30688), which was isolated from chicken breast meat and shows resistance to 10 different antimicrobials. Whole-genome and plasmid sequence analyses of this isolate will help enhance our understanding of this pathogenic multidrug-resistant serovar.

Infectious Diseases Associated with Livestock Production: Mitigating Future Risks

Humans have traveled with their livestock to the ends of the earth, and animal husbandry has transformed the face of the planet. Even as livestock provide food, these same animals have also introduced humans to new diseases. A study in this month’s EHP argues that, although it is unclear whether the intensification of livestock production will lead to a higher risk of disease emergence and transmission, some important risk factors are certainly present.1 This is especially true in contexts where changes are occurring rapidly, sometimes before regulation can catch up. “Strong regulations can do a lot to mitigate zoonotic risk,” says first author Marco Liverani, a social scientist at the London School of Hygiene & Tropical Medicine. But first, he says, we need to better understand which agricultural and economic practices promote emerging infections, if we are to identify vulnerabilities and develop effective policies to address them. For millennia livestock have shared our abodes and our diseases. The Agricultural Revolution led to the development of larger settlements and denser livestock populations. Infectious diseases that only rarely might have struck small numbers of humans in the past could now spread between animals and large numbers of people. The age of epidemics had begun.2 A 2005 study by Mark Woolhouse and Sonya Gowtage-Sequeria, infectious disease specialists at the University of Edinburgh, found that 58% of the 1,407 diseases known to infect humans were zoonotic—that is, they had originated in animals. Pathogens that could infect both animals and humans made up an even bigger proportion of emerging infectious diseases: 73%.3 “We have very intense contact with livestock. There are plenty of opportunities for the pathogens to cross over,” Woolhouse says. “There is a lot of exchange of diseases between humans and livestock in both directions.” The continued growth of the human population, combined with growing demand for animal protein, has further intensified livestock production. The danger in this, according to Liverani and colleagues, is that some practices associated with intensified production have the potential to increase the risk of zoonoses.1 Take the emergence of Nipah virus, which first appeared in Malaysia in 1999. Epidemiologists revealed that Nipah was a virus that had never been seen in humans, and ultimately traced its origins to a family of large bats known as flying foxes.4 As Malaysia’s population increased dramatically in the late twentieth century,5 farmers began growing mangoes and raising pigs in recently deforested areas. Nipah is naturally found in the fruit-eating flying foxes, which feasted on the mangoes planted by farmers. The pigs ate the mangoes that had fallen to the ground, including those that were contaminated by Nipah-laden bat saliva. The pigs caught the virus from the bats, and the humans caught the virus from the pigs.6 Although zoonotic disease is a potential issue for large industrial farming operations,7 it’s also somewhat easier to regulate these operations, given their resources and commercial status, Liverani says. Backyard farmers like the ones in Malaysia might be exposed to fewer animals, but they tend to have longer, closer contact with the animals that they do have. Close contact between humans and livestock can facilitate the exchange of diseases in both directions. According to Liverani and colleagues, the greatest risk may occur when industrial livestock operations exist alongside small family farms and wildlife populations. Liverani says contacts between livestock and wild animals can result in new pathogens entering intensive production units, where the high concentration of animals can facilitate the amplification and transmission of disease. Although the dangers of zoonoses are real, Ro McFarlane, a veterinary epidemiologist at the Australian National University in Canberra, cautions that these diseases are only one aspect of the interconnected disease risks that exist between humans, livestock, and the environment. “The intensification of food industries has also given rise to diseases that affect food production,” she says, citing another example of this interconnection. “Many of these are not zoonotic, but the effect on human health through food security and livelihoods can also be catastrophic.” McFarlane says the strength of the work by Liverani et al. is that it incorporates socioeconomic and political as well as pathogen- and farm-level risk factors into the discussion about how to manage zoonotic risk from intensive livestock industries. “This is the news,” she says—“we are making progress in doing ‘new science.’”

Herd-level relationship between antimicrobial use and presence or absence of antimicrobial resistance in gram-negative bovine mastitis pathogens on Canadian dairy farms

Concurrent data on antimicrobial use (AMU) and resistance are needed to contain antimicrobial resistance (AMR) in bacteria. The present study examined a herd-level association between AMU and AMR in Escherichia coli (n=394) and Klebsiella species (n=139) isolated from bovine intramammary infections and mastitis cases on 89 dairy farms in 4 regions of Canada [Alberta, Ontario, Québec, and Maritime Provinces (Prince Edward Island, Nova Scotia, and New Brunswick)]. Antimicrobial use data were collected using inventory of empty antimicrobial containers and antimicrobial drug use rate was calculated to quantify herd-level AMU. Minimum inhibitory concentrations (MIC) were determined using Sensititre National Antimicrobial Resistance Monitoring System (NARMS) gram-negative MIC plate (Trek Diagnostic Systems Inc., Cleveland, OH). Isolates were classified as susceptible, intermediate, or resistant. Intermediate and resistant category isolates were combined to form an AMR category, and multivariable logistic regression models were built to determine herd-level odds of AMR to tetracycline, ampicillin, cefoxitin, chloramphenicol, trimethoprim-sulfamethoxazole combination, sulfisoxazole, streptomycin and kanamycin in E. coli isolates. In the case of Klebsiella species isolates, logistic regression models were built for tetracycline and sulfisoxazole; however, no associations between AMU and AMR in Klebsiella species were observed. Ampicillin-intermediate or -resistant E. coli isolates were associated with herds that used intramammarily administered cloxacillin, penicillin-novobiocin combination, and cephapirin used for dry cow therapy [odds ratios (OR)=26, 32, and 189, respectively], and intramammary ceftiofur administered for lactating cow therapy and systemically administered penicillin (OR=162 and 2.7, respectively). Use of systemically administered penicillin on a dairy farm was associated with tetracycline and streptomycin-intermediate or -resistant E. coli isolates (OR=5.6 and 2.8, respectively). Use of cephapirin and cloxacillin administered intramammarily for dry cow therapy was associated with increasing odds of having at least 1 kanamycin-intermediate or -resistant E. coli isolate at a farm (OR=8.7 and 9.3, respectively). Use of systemically administered tetracycline and ceftiofur was associated with cefoxitin-intermediate or -resistant E. coli (OR=0.13 and 0.16, respectively); however, the odds of a dairy herd having at least 1 cefoxitin-intermediate or -resistant E. coli isolate due to systemically administered ceftiofur increased with increasing average herd parity (OR=3.1). Association between herd-level AMU and AMR in bovine mastitis coliforms was observed for certain antimicrobials. Differences in AMR between different barn types and geographical regions were not observed.

Antimicrobial sensitivity patterns of cerebrospinal fluid (CSF) isolates in Namibia: implications for empirical antibiotic treatment of meningitis.

ObjectiveBacterial meningitis is a medical emergency associated with high mortality rates. Cerebrospinal fluid (CSF) culture is the “gold standard” for diagnosis of meningitis and it is important to establish the susceptibility of the causative microorganism to rationalize treatment. The Namibia Standard Treatment Guidelines (STGs) recommends initiation of empirical antibiotic treatment in patients with signs and symptoms of meningitis after taking a CSF sample for culture and sensitivity. The objective of this study was to assess the antimicrobial sensitivity patterns of microorganisms isolated from CSF to antibiotics commonly used in the empirical treatment of suspected bacterial meningitis in Namibia.MethodsThis was a cross-sectional descriptive study of routinely collected antibiotic susceptibility data from the Namibia Institute of Pathology (NIP) database. Results of CSF culture and sensitivity from January 1, 2009 to May 31, 2012, from 33 state hospitals throughout Namibia were analysed.ResultsThe most common pathogens isolated were Streptococcus species, Neisseria meningitidis, Haemophilus influenzae, Staphylococcus, and Escherichia coli. The common isolates from CSF showed high resistance (34.3% –73.5%) to penicillin. Over one third (34.3%) of Streptococcus were resistance to penicillin which was higher than 24.8% resistance in the United States. Meningococci were susceptible to several antimicrobial agents including penicillin. The sensitivity to cephalosporins remained high for Streptococcus, Neisseria, E. coli and Haemophilus. The highest percentage of resistance to cephalosporins was seen among ESBL K. pneumoniae (n = 7, 71%–100%), other Klebsiella species (n = 7, 28%–80%), and Staphylococcus (n = 36, 25%–40%).ConclusionsThe common organisms isolated from CSF were Streptococcus Pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Staphylococcus, and E. coli. All common organisms isolated from CSF showed high sensitivity to cephalosporins used in the empirical treatment of meningitis. The resistance of the common isolates to penicillin is high. Most ESBL K. pneumoniae were isolated from CSF samples drawn from neonates and were found to be resistant to the antibiotics recommended in the Namibia STGs. Based on the above findings, it is recommended to use a combination of aminoglycoside and third-generation cephalosporin to treat non–ESBL Klebsiella isolates. Carbapenems (e.g., meropenem) and piperacillin/tazobactam should be considered for treating severely ill patients with suspected ESBL Klebsiella infection. Namibia should have a national antimicrobial resistance surveillance system for early detection of antibiotics that may no longer be effective in treating meningitis and other life-threatening infections due to resistance.

Antimicrobial resistance among respiratory Haemophilus influenzae isolates from pulmonology services over a six-year period

Respiratory tract infections (RTI) are frequently caused by Haemophilus influenzae. Widespread antibacterial resistance among respiratory microorganisms complicates empirical RTI treatment. Therefore, national data on antibiotic resistance for H. influenzae are important for guiding optimal antibiotic choice. The antibiotic susceptibility of H. influenzae strains isolated from respiratory specimens of patients admitted to the pulmonology services between 2005 and 2010 was assessed. Isolates were collected annually from 13 hospitals in the Netherlands as part of the national intramural antimicrobial resistance surveillance performed by the Dutch Working Group on Antibiotic Policy (SWAB). Breakpoints for resistance were in accordance with the criteria of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Trend analysis was performed using logistic regression analysis. In total, 1606 H. influenzae strains were analyzed. The prevalence of antibiotic resistance to amoxicillin, co-amoxiclav, doxycycline, co-trimoxazole, and clarithromycin was stable over the 6-y period, and there was a trend towards a decrease in the prevalence of beta-lactamase-producing isolates. Regarding prevalences, no significant trends were observed. Our study showed no significant changes in antibiotic resistance for H. influenzae isolated at different hospitals in the Netherlands over a 6-y period. Regular surveillance remains important in controlling the prevalence of resistance, since actual resistance data should be taken into account when the choice of an empiric antibiotic is made.