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Thesis advisor: Roche P. John / The growing threat of antibiotic resistance makes it extremely important that citizens be informed about the risks posed by antibiotic-resistant bacteria, and measures with which they can reduce these risks. The print media are major sources of such information for members of the public. In the present study, articles from major newspapers in the United States and Canada appearing between 1998 and 2002 were surveyed to determine the extent to which mention was made of antibiotic resistance and the risks associated with antibiotic resistance, the contextual precision with which this information was communicated, and the extent to which information was presented about causes, and risk-reduction measures, associated with antibiotic resistance. The majority of articles surveyed mentioned antibiotic resistance, but most failed to mention associated risks (i.e., the risk of illness and/or the risk of mortality). Articles that did report risks, did so only at a low level of contextual precision. A relatively low percentage of articles mentioned causes of antibiotic resistance, and even fewer mentioned risk reduction measures. These findings suggest that the print media could improve the efficacy with which they inform the public about issues associated with antibiotic resistance. / Thesis (BS) — Boston College, 2003. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Biology. / Discipline: College Honors Program.

Faecal pollution regularly contaminates surface waters, introducing microorganisms, including bacteria and bacteria resistant to antibiotics, to coastal waters. People can come into contact with these potentially harmful microbes when they enjoy recreational activities in the sea. Understanding the risk to bathers of acquiring infections from the sea is important for developing effective intervention strategies to protect human health. This thesis consists of four original studies which aim to answer the question ‘are bacteria in the coastal zone a threat to human health’? First, we describe a systematic review on the risk of acquiring infections from recreational use of coastal waters. Synthesising risk estimates of reporting various symptoms of ill health, we quantify this risk as well as appraise the evidence that these infections are acquired from bathing in coastal waters. The results of the second study - a large online survey - corroborate these findings and provide updated estimates of risk for UK bathers. Third, we assess the risk of ingesting antibiotic resistant bacteria among UK coastal water users. In the final study, we measured the prevalence of faecal carriage of antibiotic resistant bacteria among a highly exposed group – surfers, and in an unexposed group (non-surfers). We conclude that despite improvements made to the collection, treatment and discharge of sewage, and initiatives to communicate water quality to members of the public in recent years, people who bathe in coastal waters are still at an increased risk of adverse health outcomes, whether this is experiencing symptoms of ill health, or exposure to and colonisation by antibiotic resistant bacteria.

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Introduction and Justification: Diarrheal disease is a leading cause of death in children in low- and moderate-income countries. Food, food waste, and water are all vehicles that can promote the spread of diarrheal disease-causing bacteria like Campylobacter, Salmonella enterica, and E. coli. Resistance to commonly used antibiotics is on the rise, making them difficult to manage. This study aimed to determine prevalence and antibiotic resistance profiles of Campylobacter, S. enterica, and E. coli isolated from food, food waste, and water samples obtained from the Chobe Region of Botswana. In addition, the survival of two common pathogens, E. coli and C. jejuni, on kale, a type of leafy green commonly consumed raw, was determined. Methods: Samples were collected from the Chobe region of Botswana in 2022 including water from the local river, food (produce, beef, pork, and poultry) from local vendors, and food scraps from the landfill. Food samples were enriched in the appropriate selective media: Brilliant Green Bile Broth for E. coli, Bolton Broth for Campylobacter, and Rappaport Vassiliadis Broth for S. enterica. Water samples were collected using modified USEPA methods1103.1 and 1604, E.coli isolation was performed by plating on RAPID E.coli2 agar and incubation at 37°C for 2h and 44°C for 16-22h. Campylobacter, S. enterica, and E. coli were isolated from meat, poultry, and water samples before being sent to Virginia Tech, while enriched bacterial pellets from the produce were shipped for screening and isolation at Virginia Tech. E.coli were confirmed by PCR detecting the phoA gene (all E. coli), and classified as pathogenic through screening for the eae (present in enterohemorrhagic and enteropathogenic E.coli), stx1 and stx2 (present in enterohemorrhagic E. coli) and est1b ( present in Enterotoxigenic E.coli) genes. Campylobacter isolates were confirmed using a genera-specific PCR while S. enterica isolates were confirmed using invA primers. These enrichment and primer sets were tested as part of a study to determine the survival of E. coli O157:H7 and C. jejuni on kale during a 21-day shelf life. E. coli and S. enterica isolates were subjected to antibiotic resistance testing using the Kirby-Bauer Disk Diffusion method. Results: Methods for detection of inoculated E. coli O157:H7 on kale indicated survival for the majority of the shelf-life (up to 19 d), in comparison, C. jejuni was undetectable by day 13 using enrichment and PCR or plating. From the Botswanan samples, E. coli was isolated from 20% of produce, 49% of meat, and 84.7% of water. Salmonella was only isolated from produce samples (2.4%, 7/294). Resistance was uncommon among the Salmonella isolates with only one isolate being resistant to chloramphenicol. No Campylobacter were isolated from the screened produce, meat, or food waste. E. coli resistant to 3 or more classes of antibiotics (MCR) were identified in 15.5% of produce, and 22.2% of meat isolates. Isolation of E. coli or Salmonella from meat was not associated with a particular food type. In contrast, isolation of E. coli was more common from certain types of vegetables and fruits. Antibiotic-resistant E. coli were isolated more commonly from beef, poultry, and pork than from produce. Multi-class resistant E. coli were isolated from fruits, greens, soil associated, and above ground associated vegetables, beef, and poultry. Water samples were collected from the same time period as the food samples. E. coli isolation, especially pathogens (based on eae presence) was more frequent from environmental water samples collected during the wet season compared to the dry season. Water samples collected during periods of increased rainfall were more likely to contain E. coli isolates, especially pathogens. S. enterica and Diarrheagenic E. coli isolates, especially MCR isolates, pose a significant risk of illness to consumers. Strategies to reduce the circulation of these pathogens in foods and water sources are needed. / Master of Science in Life Sciences / People can get sick with diarrheal diseases after consuming contaminated food and water. These illnesses are difficult to treat and control when the bacteria causing them are resistant to antibiotics. Campylobacter, Salmonella, and diarrheagenic E. coli are three types of bacteria that can cause illness from food and water. These illnesses disproportionately affect people, especially children, in low-and moderate-income countries like Botswana. Little is known about the prevalence of Campylobacter, Salmonella, and diarrheagenic Escherichia coli in Botswana. This study aimed to determine the prevalence of these microorganisms as well as how resistant they are to different types of antibiotics. Samples from produce, beef, poultry, pork, and recreational water sources were collected in the Chobe region of Botswana over the course of 2022. Food samples were collected from different vendors and food scraps were obtained from the landfill. E. coli and Salmonella were isolated out of meat and water samples in Botswana while produce samples were shipped as mixed cultures to Virginia Tech where E. coli, Salmonella, and Campylobacter isolation or confirmation was done. Once the target bacteria were isolated, their resistance to certain antibiotics was tested. Salmonella was only found in produce from samples collected during October-December. No Campylobacter was found from produce, meat, or food waste. More E. coli was isolated from fruit or vegetable food waste collected from the landfill than from produce bought at local vendors. E. coli was obtained from meat purchased from local vendors more often than samples from the landfill. E. coli was found more often in water when there was more rainfall. E. coli that causes illness was also more likely to be obtained during the wet seasons. Resistant E. coli that could not be killed by the screened antibiotics, were classified as multi-drug resistant when it was resistant to more than three antibiotics. Rainfall, season, and the food source influenced if E. coli isolates were likely to be multi-drug resistant. While more research is needed to determine how these bacteria are moving in the environment and gaining resistance to antibiotics, the findings of this study show they are present in the environment and require further research.

Antibiotic resistance is a growing human health threat, making infections more difficult to treat and increasing fatalities from and cost of treatment of associated diseases. The rise of multidrug resistant pathogens threatens a return to the pre-antibiotic era where even the most common infections may be impossible to treat. It is estimated that the majority of global antibiotic use, and use in the U.S., is dedicated towards livestock, where they are used to promote growth, treat, or prevent disease. Given that exposure to antibiotics selects for antibiotic resistant bacteria (ARBs) and can stimulate the horizontal transfer of their associated antibiotic resistance genes (ARGs), it is important to examine livestock operations as a reservoir of resistance. Correspondingly, there is growing interest in identifying how agricultural practices can limit the potential for spread of antibiotic resistance through the "farm to fork continuum," starting with antibiotic use practices, manure management and land application and ending with the spread of ARBs and ARGs present onto edible crops and serving as a route of exposure to consumers. This study focused specifically on the effect of composting on the prevalence of ARBs and ARGs in cattle manure. Three composting trials were performed: small-scale, heat-controlled, and large-scale. The small-scale composting trial compared dairy and beef manures, with or without antibiotic treatment (treated beef cattle received chlortetracycline, sulfamethazine, and tylosin while treated dairy cattle received cephapirin and pirlimycin), subject to either static or turned composting. The heat-controlled composting trial examined only dairy manure, with or without antibiotic treatment, subject to static composting, but using external heat tape applied to the composting tumblers to extend the duration of the thermophilic (>55°C) temperature range. The large-scale composting trial examined dairy manure, with or without antibiotic treatment, subject to static composting at a much larger scale that is more realistic to typical farm practices. Samples were analyzed to assess phenotypic resistance using the Kirby Bauer disk diffusion method and by diluting and plating onto antibiotic-supplemented agar. Genetic markers of resistance were also assessed using quantitative polymerase chain reaction (qPCR) to quantify sul1 and tet(W) ARGs; metagenomic DNA sequencing and analysis were also performed to assess and compare total ARG abundance and types across all samples. Results indicate that composting can enrich indicators of phenotypic and genetic resistance traits to certain antibiotics, but that most ARGs are successfully attenuated during composting, as evidenced by the metagenomic sequencing. Maintaining thermophilic composting temperatures for adequate time is necessary for the effective elimination of enteric bacteria. This study suggests that indicator bacteria that survive composting tend to be more resistant than those in the original raw manure; however, extending the thermophilic stage of composting, as was done in the heat-controlled trial, can reduce target indicator bacteria below detection limits. Of the two ARGs specifically quantified via qPCR, prior administration of antibiotics to cattle only had a significant impact on tet(W). There was not an obvious difference in the final antibiotic resistance profiles in the finished beef versus dairy manure composts according to metagenomics analysis. Based on these results, composting is promising as a method of attenuating ARGs, but further research is necessary to examine in depth all of the complex interactions that occur during the composting process to maximize performance. If not applied appropriately, e.g., if time and temperature guidelines are not enforced, then there is potential that composting could exacerbate the spread of certain types of antibiotic resistance. / Master of Science

The reduced efficacy of antibiotics in treating common infections is one of the most pressing health concerns of the 21st Century. Increasing evidence links the widespread use of antibiotics in livestock production to the transfer of bacteria carrying antibiotic resistance genes to the broader environment. It is therefore critical to understand the persistence and dissemination of resistance in agricultural soils to understand potential threats to consumers. The goal of this large-scale agricultural field experiment was to identify the effects of crop (lettuce, radish) and fertilizer type (inorganic, compost, raw manure) on the incidence and persistence of antibiotic-resistant fecal coliforms, a common family of fecal indicator bacteria used to track the environmental spread of antibiotic resistance. Soil samples were collected eight times over a 120-day period and analyzed for fecal coliforms utlizing a suite of MacConkey agars supplemented with different antibiotics (ceftazidime, clindamycin, erythromycin, sulfamethoxazole, and tetracycline). Given the number of samples with resistant fecal coliform concentrations below the limit of detection, analyses to identify the effects of soil treatment and crop relied on Zero-inflated Poisson Regressions. Antibiotic-resistant culturable fecal coliforms were recoverable from soils across all treatments immediately following application, though persistence throughout the experiment varied by antibiotic. Sulfamethoxazole- and tetracycline-resistant fecal coliforms were nondetectable after Day 1; this was expected, as the cattle supplying the manure amendments were not treated with these antibiotics or similar analogs. Clindamycin- and erythromycin-resistant fecal coliforms were nondetectable after 42 days but rebounded on Day 90 in the soil; both of these drugs were of the same antibiotic class as the ones used to treat the dairy cattle during the manure collection period. Ceftazidime-resistant fecal coliform levels were consistently high throughout the duration of the growing season. No statistical differences were observed between root and aboveground crops. Results suggest that soils amended with raw or composted dairy manure are at risk of contamination with antibiotic resistant fecal coliforms; however, composting decreased the antibiotic resistant fecal coliform levels of the macrolide (erythromycin) and lincosamide (clindamycin) antibiotic classes administered to the dairy cattle (cephapirin and pirlimycin). / Master of Science

Antibiotic-resistant bacteria(ARB) is causing increased health risk and cost to society. Mathematical models have been developed to study the transmission of resistant bacteria and the efficacy of preventive measures to slow its spread within a hospital setting. The majority of these models have assumed a constant total hospital population with the admission and discharge rates being equal throughout the duration. But a typical hospital population varies from day to day and season to season. In this thesis, we apply variable admission and discharge daily rates to existing deterministic and stochastic models which examine the transmission of single and dual resistant bacteria. We perform stability and equilibrium analyses as well as a sensitivity analysis on the resulting model..

Smittsamma sjukdomar kostar det svenska samhället enorma summor varje år. Behandlingen av smittade patienter har tidigare uppskattats till 5-10 miljarder svenska kronor årligen. Vidare estimeras de förebyggande åtgärderna kosta samhället runt en miljard svenska kronor. Detta betyder att det finns en ekonomisk drivkraft för att reducera antalet smittade patienter inom vården, speciellt de fall som är orsakade av resistenta bakterier. Samtidigt pågår det en debatt om resistenta bakterier och antibiotikaförbrukningen i både forskning och media. Resistenta bakterier kan bli ett hot mot vår framtid om vi inte minskar antibiotikaförbrukningen och vidtar åtgärder för att förhindra smittspridning. Om antalet personer som blir smittade av resistenta bakterier kan reduceras minskar även antibiotikaförbrukningen som i sin tur leder till att färre bakterier utvecklar ett resistensmönster för antibiotika. Detta betyder att det är viktigt att studera och effektivisera hanteringen av smittsamma patienter.   För att reducera antalet smittade patienter måste förebyggande åtgärder vidtas och smittkällan måste kartläggas vid ett upptäckt fall av en smitta. Svensk sjukvård arbetar idag aktivt med smitthantering. Detta begrepp omfattar upptäckt, kontroll och spårning av smitta. Uppdragsgivaren till detta examensarbete, Cambio Healthcare Systems, saknar en fullständig bild över hur smitthanteringen egentligen går till på ett sjukhus. Deras målsättning är att utveckla ett IT-system som kan underlätta smitthanteringsprocessen. Denna studie syftar till att kartlägga informationsflödet vid smitthanteringsprocessen och identifiera de inblandade aktörernas ansvarsområden och skyldigheter enligt regelverket. Vidare syftar arbetet till att presentera åtgärdsförslag som kan minska de identifierade riskerna och effektivisera smitthanteringsprocessen av resistenta bakterier.   För att kartlägga smitthanteringsprocessen genomfördes en fallstudie av ett svenskt universitetssjukhus under våren 2013. Aktörer som studerades var det mikrobiologiska laboratoriet, vårdhygien, smittskyddsenheten, smittskyddsinstitutet samt läkare och sjuksköterskor vid två avdelningar på sjukhuset. Datainsamlingen består av intervjuer, observationer och dokument.   Resultatet av fallstudien visade att smitthanteringsprocessen är ett komplext system med ett omfattande informationsflöde. Huvudaktörerna är vårdhygien, sjukvårdspersonalen och det mikrobiologiska laboratoriet. De är viktiga eftersom deras praktiska handlande är avgörande för att smitthanteringen genomförs. Smittskyddsenheten är inblandad till viss del, men tillhör inte huvudaktörerna. Studien visade även att smittskyddsinstitutet inte hade någon framträdande roll i smitthanteringsprocessen av resistenta bakterier på sjukhuset.   Ansvarsfördelningen är till viss del styrd av smittskyddslagen och enligt denna lag har den behandlande läkaren en central roll i processen. I verkligheten är läkarens roll mindre framträdande vid smittspårningen, vanligtvis delegerar läkaren uppgifter till sjuksköterskor eller till vårdhygien. Mycket av kommunikationen mellan aktörerna är muntlig och detta innebär att ett flertal risker kan uppstå. Vid identifieringen av risker för hela processen konstaterades det att de flesta risker kan uppstå på grund av den mänskliga faktorn, ofta i kombination med användandet av ett otillräckligt datasystem. Åtgärdsförslagen för att effektivisera processen fokuserar därför på att minimera de identifierade riskerna med hjälp av framtida IT-system.   Slutsatsen av studien är att det finns ett stort behov av IT-lösningar för att effektivisera smitthanteringsprocessen av resistenta bakterier. Min rekommendation är att Cambio Healthcare Systems AB bör fokusera på att utveckla ett system för att digitalisera arkiveringen av beläggningslistorna och spåra patientflöden tillbaka i tiden i Cosmic då detta är ett starkt önskemål från kunderna. En annan viktig åtgärd är att utveckla smittspecifika checklistor som visas på datorn i samband med att läkaren får ett positivt provsvar. Slutligen rekommenderar jag Cambio Healthcare Systems AB att utveckla ett smittlarm som kan integreras med deras befintliga whiteboardtavla som nyligen lanserades. / Infectious diseases are a major cost item for the Swedish society. The treatment of infected patients has previously been estimated to 5-10 billion SEK annually and preventive actions cost the Swedish society around one billion SEK every year. Therefore, there are strong economic incentives to reduce the number of infected patients in care, particularly cases caused by resistant bacteria. There is an ongoing debate in both media and research about bacterial resistance and antibiotic consumption. Resistant bacteria can be a threat to our future if we do not reduce the consumption of antibiotics and take measure against infection spreading. If it is possible to reduce the number of resistant bacteria infected patients in the future it enables a decline in antibiotic consumption. This in turn leads to a decreased quantity of bacteria that is able to develop a resistance pattern to antibiotic. Thus, it is highly motivated to study and streamline the process of infection control.   Preventive measures must be taken and the source of the infection must be identified in order to reduce the number of infected patients. The Swedish health care sector is currently working actively with infection control. The concept of infection control encloses the detection, the control and the tracing of the infection. The requestor of this master thesis, Cambio Healthcare Systems AB, does not have a complete picture of the process of the infection control. Their goal is to develop an IT system to facilitate the process of infection control. This study aims to map the information flow of the process and to identify the involved actors’ field of responsibility and obligations according to the law. Further, this thesis aims to present action proposals that can reduce the identified risks and streamline the infection control of resistant bacteria.   A case study of a Swedish university hospital was performed in the spring of 2013 in order to map the process of infection control. The investigated actors were the microbiological laboratory, the local health protection unit (Vårdhygien), the unit of infection control at a regional level (Smittskyddsenheten), the Swedish Institute of Infectious Disease Control (Smittskyddsinstitutet) and physicians and nurses at two hospital departments. The data collection consists of interviews, observations and documents.   The result of this case study shows that the process of infection control is a complex system with an extensive flow of information. The main actors are the local health protection unit, the microbiological laboratory and the medical staff. Their practical actions are essential for the process of infection control. The unit of infection control at a regional level is involved to some extent, but does not belong to the main actors. Furthermore, the study showed that the Swedish Institute of Infectious Disease Control does not have a prominent role in the process at the hospital.   The division of responsibilities is to some extent controlled by the law. According to the law, the physician in charge has a central role in the process of infection control. However, the physician’s role in reality is less prominent. Usually, the physician delegates the tasks to the other actors such as nurses or to the local health protection unit. The communication between the actors is mainly oral and this can cause risks. Most of the identified risks occurred due to human error, often in combination with use of an insufficient IT-system. Therefore, the proposed actions to streamline the process focus on minimizing the identified risks with help of future IT solutions.   The conclusion of this study is that there is a strong demand for IT solutions to streamline the process of infection control of resistant bacteria. My recommendation is that Cambio Healthcare Systems AB should focus on developing a system to digitalize the archiving of the occupancy lists, which also enables tracing the flow of patients back in time. This is a request from several health care professionals. Another important proposed action is to develop a checklist that is specific for every infection disease. Simultaneously as the physician receives the positive test results, this checklist will appear on the physician’s screen. Finally, I recommend Cambio Healthcare Systems AB to develop an alarm to infection diseases that can be integrated with their existing whiteboards that were recently introduced to the market.

The extensive medical and agricultural use and misuse of antibiotics during the last 70 years has caused an enrichment of resistant pathogenic bacteria that now severely threatens our capacity to efficiently treat bacterial infections. While is has been known for a long time that high concentrations of antibiotics can select for resistant mutants, less is known about the lower limit at which antibiotics can be selective and enrich for resistant bacteria. In this thesis we investigated the role of low concentrations of antibiotics and heavy metals in the enrichment and evolution of antibiotic resistance. Selection was studied using Escherichia coli and Salmonella enterica serovar Typhimurium LT2 with different resistance mutations, different chromosomal resistance genes as well as large conjugative multidrug resistance plasmids. Using very sensitive competition experiments, we showed that antibiotic and heavy metal levels more than several hundred-fold below the minimal inhibitory concentration of susceptible bacteria can enrich for resistant bacteria. Additionally, we demonstrated that subinhibitory levels of antibiotics can select for de novo resistant mutants, and that these conditions can select for a new spectrum of low-cost resistance mutations. The combinatorial effects of antibiotics and heavy metals can cause an enrichment of a multidrug resistance plasmid, even if the concentration of each compound individually is not high enough to cause selection. These results indicate that environments contaminated with low levels of antibiotics and heavy metals such as, for example, sewage water or soil fertilized with sludge or manure, could provide a setting for selection, enrichment and transfer of antibiotic resistance genes. This selection could be a critical step in the transfer of resistance genes from environmental bacteria to human pathogens.