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  • Möller, Vidar; Östholm-Balkhed, Åse; Berild, Dag; Fredriksson, Mats; Gottfredsson, Magnus; Holmbom, Martin; Järvinen, Asko; Kristjansson, Mar; Rydell, Ulf; Sonksen, Ute Wolff; Kolmos, Hans Joern; Hanberger, Håkan (2021)
    Background The Nordic countries have comparable nationwide antibiotic resistance surveillance systems and individual antibiotic stewardship programmes. The aim of this study was to assess antibiotic resistance among major pathogens in relation to practice guidelines for hospital antibiotic treatment and antibiotic use in Nordic countries 2010-2018. Methods Antibiotic resistance among invasive isolates from 2010-2018 and aggregated antibiotic use were obtained from the European Centre for Disease Prevention and Control. Hospital practice guidelines were obtained from national or regional guidelines. Results Antibiotic resistance levels among Escherichia coli and Klebsiella pneumoniae were similar in all Nordic countries in 2018 and low compared to the European mean. Guidelines for acute pyelonephritis varied; 2nd generation cephalosporin (Finland), 3rd generation cephalosporins (Sweden, Norway), ampicillin with an aminoglycoside or aminoglycoside monotherapy (Denmark, Iceland and Norway). Corresponding guidelines for sepsis of unknown origin were 2nd (Finland) or 3rd (Sweden, Norway, Iceland) generation cephalosporins, carbapenems, (Sweden) combinations of penicillin with an aminoglycoside (Norway, Denmark), or piperacillin-tazobactam (all Nordic countries). Methicillin-resistant Staphylococcus aureus rates were 0-2% and empirical treatment with anti-MRSA antibiotics was not recommended in any country. Rates of penicillin non-susceptibility among Streptococcus pneumoniae were low (
  • Muurinen, Johanna; Muziasari, Windi I.; Hultman, Jenni; Pärnänen, Katariina; Narita, Vanny; Lyra, Christina; Fadlillah, Lintang N.; Rizki, Ludhang P.; Nurmi, William; Tiedje, James M.; Dwiprahasto, Iwan; Hadi, Pramono; Virta, Marko P. J. (2022)
    Water and sanitation are important factors in the emergence of antimicrobial resistance in low-and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and enfluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.
  • Tiwari, Ananda; Gomez-Alvarez, Vicente; Siponen, Sallamaari; Sarekoski, Anniina; Hokajärvi, Anna-Maria; Kauppinen, Ari; Torvinen, Eila; Miettinen, Ilkka T.; Pitkänen, Tarja (2022)
    Information on the co-occurrence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) among bacterial communities in drinking water distribution systems (DWDSs) is scarce. This study characterized ARGs and MRGs in five well-maintained DWDSs in Finland. The studied DWDSs had different raw water sources and treatment methods. Two of the waterworks employed artificially recharged groundwater (ARGW) and used no disinfection in the treatment process. The other three waterworks (two surface and one groundwater source) used UV light and chlorine during the treatment process. Ten bulk water samples (two from each DWDS) were collected, and environmental DNA was extracted and then sequenced using the Illumina HiSeq platform for high-throughput shotgun metagenome sequencing. A total of 430 ARGs were characterized among all samples with the highest diversity of ARGs identified from samples collected from non-disinfected DWDSs. Furthermore, non-disinfected DWDSs contained the highest diversity of bacterial communities. However, samples from DWDSs using disinfectants contained over double the ratio of ARG reads to 16S rRNA gene reads and most of the MRG (namely mercury and arsenic resistance genes). The total reads and types of ARGs conferring genes associated with antibiotic groups namely multidrug resistance, and bacitracin, beta-lactam, and aminoglycoside and mercury resistance genes increased in waterworks treating surface water with disinfection. The findings of this study contribute toward a comprehensive understanding of ARGs and MRGs in DWDSs. The occurrence of bacteria carrying antibiotic or metal resistance genes in drinking water causes direct exposure to people, and thus, more systematic investigation is needed to decipher the potential effect of these resistomes on human health.
  • Skarp, C. P. A.; Hanninen, M-L; Rautelin, Hilpi I (2016)
    The incidence of human infections caused by Campylobacter jejuni and Campylobacter coil, the main bacterial agents of gastrointestinal disease, has been increasing worldwide. Here, we review the role of poultry as a source and reservoir for Campylobacter. Contamination and subsequent colonization of broiler flocks at the farm level often lead to transmission of Campylobacter along the poultry production chain and contamination of poultry meat at retail. Yet Cainpylobacter prevalence in poultry, as well as the contamination level of poultry products, vary greatly between different countries so there are differences in the intervention strategies that need to be applied. Temporal patterns in poultry do not always coincide with those found in human infections. Studies in rural and urban areas have revealed differences in Campylobacter infections attributed to poultry, as poultry seems to be the predominant reservoir in urban, but not necessarily in rural, settings. Furthermore, foreign travel is considered a major risk factor in acquiring the disease, especially for individuals living in the northern European countries. Intervention strategies aimed at reducing Campylobacter colonization in poultry and focused at the farm level have been successful in reducing the number of Campylobacter cases in several countries. Increasing farm biosecurity and education of consumers are likely to limit the risk of infection. Overall, poultry is an important reservoir and source of human campylobacteriosis, although the contribution of other sources, reservoirs and transmission warrants more research. Clinical Microbiology and Infection (C) 2015 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.
  • Thomson, Katariina; Eskola, Katarina; Eklund, Marjut; Suominen, Kristiina; Maatta, Merita; Junnila, Jouni; Nykasenoja, Suvi; Niinisto, Kati; Gronthal, Thomas; Rantala, Merja (2022)
    Background Extended-spectrum beta-lactamase producing Enterobacterales (ESBL-E) are important causative agents for infections in humans and animals. At the Equine Veterinary Teaching Hospital of the University of Helsinki, the first infections caused by ESBL-E were observed at the end of 2011 leading to enhanced infection surveillance. Contact patients were screened for ESBL-E by culturing infection sites and rectal screening. This study was focused on describing the epidemiology and microbiological characteristics of ESBL-E from equine patients of the EVTH during 2011-2014, and analysing putative risk factors for being positive for ESBL-E during an outbreak of Klebsiella pneumoniae ST307. Results The number of ESBL-E isolations increased through 2012-2013 culminating in an outbreak of multi-drug resistant K. pneumoniae ST307:bla(CTX-M-1):bla(TEM):bla(SHV) during 04-08/2013. During 10/2011-05/2014, altogether 139 ESBL-E isolates were found from 96 horses. Of these, 26 were from infection-site specimens and 113 from rectal-screening swabs. A total of 118 ESBL-E isolates from horses were available for further study, the most numerous being K. pneumoniae (n = 44), Escherichia coli (n = 31) and Enterobacter cloacae (n = 31). Hospital environmental specimens (N = 47) yielded six isolates of ESBL-E. Two identical E. cloacae isolates originating from an operating theatre and a recovery room had identical or highly similar PFGE fingerprint profiles as five horse isolates. In the multivariable analysis, mare-foal pairs (OR 4.71, 95% CI 1.57-14.19, P = 0.006), length of hospitalisation (OR 1.62, 95% CI 1.28-2.06, P < 0.001) and passing of a nasogastric tube (OR 2.86, 95% CI 1.03-7.95, P = 0.044) were associated with being positive for ESBL-E during the K. pneumoniae outbreak. Conclusions The occurrence of an outbreak caused by a pathogenic ESBL-producing K. pneumoniae ST307 strain highlights the importance of epidemiological surveillance of ESBL-E in veterinary hospitals. Limiting the length of hospitalisation for equine patients may reduce the risk of spread of ESBL-E. It is also important to acknowledge the importance of nasogastric tubing as a potential source of acquiring ESBL-E. As ESBL-E were also found in stomach drench pumps used with nasogastric tubes, veterinary practices should pay close attention to appropriate equipment cleaning procedures and disinfection practices.
  • Larsson, D. G. Joakim; Andremont, Antoine; Bengtsson-Palme, Johan; Brandt, Kristian Koefoed; Husman, Ana Maria de Roda; Fagerstedt, Patriq; Fick, Jerker; Flach, Carl-Fredrik; Gaze, William H.; Kuroda, Makoto; Kvint, Kristian; Laxminarayan, Ramanan; Manaia, Celia M.; Nielsen, Kaare Magne; Plant, Laura; Ploy, Marie-Cecile; Segovia, Carlos; Simonet, Pascal; Smalla, Kornelia; Snape, Jason; Topp, Edward; van Hengel, Arjon J.; Verner-Jeffreys, David W.; Virta, Marko P. J.; Wellington, Elizabeth M.; Wernersson, Ann-Sofie (2018)
    There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.(1)
  • Oikarainen, Paula E.; Pohjola, Leena K.; Pietola, Eeva S.; Heikinheimo, Annamari (2019)
    Extended-spectrum beta-lactamase (ESBL) and plasmidic AmpC (pAmpC) producing Escherichia coli are found in the poultry production even without antibiotic use. The spread of these bacteria has been suggested to occur via imported parent birds, enabling transmission to production level broilers vertically via eggs. We studied transmission of ESBL/pAmpC-producing E. coli and E. coli without antibiotic selection by sampling imported parent birds (n = 450), egg surfaces prior to and after the incubation period (n = 300 and n = 428, respectively) and the laying house environment (n = 20). Samples were additionally taken from embryos (n = 422). To study the prevention of transmission, a competitive exclusion (CE) solution was added onto freshly laid eggs prior to incubation period (n = 150). Results showed carriage of ESBL/pAmpC-producing E. coil in parent birds (26.7%), the environment (5%) and egg surfaces before the incubation period (1.3%), but not from egg surfaces or embryos after the incubation period. Whole genome sequencing revealed ESBL/pAmpC-producing E. coil isolates belonging to clonal lineages ST429 and ST2040. However, the finding of E. coli cultured without antibiotic selection in two (2.2%) embryos strengthens the need to study E. coil transmission in poultry production in more depth. Since ESBL/pAmpC-producing E. coli seem not to persist on egg surfaces, there is no need to use CE solution ex ovo as a prevention method. The results indicate that other routes, such as for example transmission through fomites or horizontal gene transfer by other bacterial species, could be more important than vertical transmission in the spread of resistance in broiler production.
  • Parnanen, Katariina M. M.; Hultman, Jenni; Markkanen, Melina; Satokari, Reetta; Rautava, Samuli; Lamendella, Regina; Wright, Justin; McLimans, Christopher J.; Kelleher, Shannon L.; Virta, Marko P. (2022)
    Background Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) are present in high numbers in antibiotic-naive infants' gut microbiomes, and infant mortality caused by resistant infections is high. The role of antibiotics in shaping the infant resistome has been studied, but there is limited knowledge on other factors that affect the antibiotic resistance burden of the infant gut. Objectives Our objectives were to determine the impact of early exposure to formula on the ARG load in neonates and infants born either preterm or full term. Our hypotheses were that diet causes a selective pressure that influences the microbial community of the infant gut, and formula exposure would increase the abundance of taxa that carry ARGs. Methods Cross-sectionally sampled gut metagenomes of 46 neonates were used to build a generalized linear model to determine the impact of diet on ARG loads in neonates. The model was cross-validated using neonate metagenomes gathered from public databases using our custom statistical pipeline for cross-validation. Results Formula-fed neonates had higher relative abundances of opportunistic pathogens such as Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Klebsiella oxytoca, and Clostridioides difficile. The relative abundance of ARGs carried by gut bacteria was 69% higher in the formula-receiving group (fold change, 1.69; 95% CI: 1.12-2.55; P = 0.013; n = 180) compared to exclusively human milk-fed infants. The formula-fed infants also had significantly less typical infant bacteria, such as Bifidobacteria, that have potential health benefits. Conclusions The novel finding that formula exposure is correlated with a higher neonatal ARG burden lays the foundation that clinicians should consider feeding mode in addition to antibiotic use during the first months of life to minimize the proliferation of antibiotic-resistant gut bacteria in infants.
  • Lebreton, Francois; van Schaik, Willem; McGuire, Abigail Manson; Godfrey, Paul; Griggs, Allison; Mazumdar, Varun; Corander, Jukka; Cheng, Lu; Saif, Sakina; Young, Sarah; Zeng, Qiandong; Wortman, Jennifer; Birren, Bruce; Willems, Rob J. L.; Earl, Ashlee M.; Gilmore, Michael S. (2013)
  • Kantele, Anu; Lääveri, Tinja (2022)
    Background: Antibiotics are no longer the primary approach for treating all travellers' diarrhoea (TD): most cases resolve without antibiotics and using them predisposes to colonization by multidrug-resistant bacteria. Data are accumulating on increasing resistance among TD pathogens, yet research into the most common agents, diarrhoeagenic Escherichia coli (DEC), remains limited. Methods: A total of 413 travellers to the (sub)tropics were analyzed for travel-acquired diarrhoeal pathogens and ESBL-PE. To identify ESBL-producing DEC, ESBL-producing E. coli (ESBL-EC) isolates were subjected to multiplex qPCR for various DEC pathotypes: enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroinvasive (EIEC) and enterohaemorrhagic (EHEC) E. coli. For a literature review, we screened studies among travellers and locals in low- and middle-income countries (LMICs) on the frequency of ESBL-producing DEC, and among travellers, also DEC with resistance to ciprofloxacin, azithromycin, and rifamycin derivatives. Results: Our rate of ESBL-EC among all DEC findings was 2.7% (13/475); among EAEC 5.7% (10/175), EPEC 1.1% (2/180), ETEC 1.3% (1/80) and EHEC (0/35) or EIEC 0% (0/5). The literature search yielded three studies reporting ESBL-EC frequency and thirteen exploring resistance to TD antibiotics among travel-acquired DEC. For EAEC and ETEC, the ESBL-EC rates were 10-13% and 14-15%, resistance to fluoroquinolones 0-42% and 0-40%, azithromycin 0-29% and 0-61%, and rifaxim in 0% and 0-20%. The highest rates were from the most recent collections. Proportions of ESBL-producing DEC also appear to be increasing among locals in LMICs and even carbapenemase-producing DEC were reported. Conclusion: ESBL producers are no longer rare among DEC, and the overall resistance to various antibiotics is increasing. The data predict decreasing efficacy of antibiotic treatment, threatening its benefits, for disadvantages still prevail when efficacy is lost.
  • Palma, Federica; Manfreda, Gerardo; Silva, Mickael; Parisi, Antonio; Barker, Dillon O. R.; Taboada, Eduardo N.; Pasquali, Frederique; Rossi, Mirko (2018)
    Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- has been associated with food-borne epidemics worldwide and swine appeared to be the main reservoir in most of the countries of isolation. However, the monomorphic nature of this serovar has, so far, hindered identification of the source due to expansion of clonal lineages in multiple hosts and food producing systems. Since geographically structured genetic signals can shape bacterial populations, identification of biogeographical markers in S. 1,4,[5],12:i:- genomes can contribute to improving source attribution. In this study, the phylogeographical structure of 148 geographically and temporally related Italian S. 1,4,[5],12:i:- has been investigated. The Italian isolates belong to a large population of clonal S. Typhimurium/1,4,[5],12:i:- isolates collected worldwide in two decades showing up to 2.5% of allele differences. Phylogenetic reconstruction revealed that isolates from the same geographical origin form highly supported monophyletic groups, suggesting discrete geographical segregation. These monophyletic groups are characterized by the gene content of a large sopE-containing prophage. Within this prophage, genome-wide comparison identified several genes overrepresented in strains of Italian origin. This suggests that certain lineages may be characterized by the acquisition of specific accessory genetic markers useful for improving identification of the source in ongoing epidemics.
  • Murphy, Robert; Palm, Martin; Mustonen, Ville; Warringer, Jonas; Farewell, Anne; Parts, Leopold; Moradigaravand, Danesh (2021)
    Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestockand human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections. IMPORTANCE Escherichia coli is a clinically important bacterial species implicated in humanand livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.
  • Castro, Hanna; Jaakkonen, Anniina; Hakakorpi, Anna; Hakkinen, Marjaana; Isidro, Joana; Korkeala, Hannu; Lindström, Miia; Hallanvuo, Saija (2019)
    Packaged raw milk contaminated with Yersinia pseudotuberculosis mediated a large yersiniosis outbreak in southern Finland in 2014. The outbreak was traced back to a single dairy farm in southern Finland. Here we explore risk factors leading to the outbreak through epidemiologic investigation of the outbreak farm and through genomic and phenotypic characterization of the farm's outbreak and non-outbreak associated Y. pseudotuberculosis strains. We show that the outbreak strain persisted on the farm throughout the 7-month study, whereas the non-outbreak strains occurred sporadically. Phylogenomic analysis illustrated that the outbreak strain was related to previously published genomes of wild animal isolates from Finland, implying that wild animals were a potential source of the outbreak strain to the farm. We observed allelic differences between the farm's outbreak and non-outbreak strains in several genes associated with virulence, stress response and biofilm formation, and found that the outbreak strain formed biofilm in vitro and maintained better growth fitness during cold stress than the non-outbreak strains. Finally, we demonstrate the rapid growth of the outbreak strain in packaged raw milk during refrigerated storage. This study provides insight of the risk factors leading to the Y. pseudotuberculosis outbreak, highlights the importance of pest control to avoid the spread of pathogens from wild to domestic animals, and demonstrates that the cold chain is insufficient as the sole risk management strategy to control Y. pseudotuberculosis risk associated with raw drinking milk.
  • Sartelli, Massimo; Coccolini, Federico; Abu-Zidan, Fikri M.; Ansaloni, Luca; Bartoli, Stefano; Biffl, Walter; Borghi, Felice; Chouillard, Elie; Cui, Yunfeng; Nascimento, Rafael De Oliveira; De Simone, Belinda; Di Saverio, Salomone; Duane, Therese; Eckmann, Christian; Eid, Hani O.; Gomes, Carlos Augusto; Gomes, Felipe Couto; Hecker, Andreas; Hecker, Birgit; Isik, Arda; Itani, Kamal M. F.; Leppäniemi, Ari; Litvin, Andrey; Luppi, Davide; Maier, Ronald; Manzano-Nunez, Ramiro; Marwah, Sanjay; Mazuski, John; Moore, Ernest; Perrone, Gennaro; Rasa, Kemal; Rubio, Ines; Sawyer, Robert; Labricciosa, Francesco M.; Catena, Fausto (2020)
    Appropriate measures of infection prevention and management are integral to optimal clinical practice and standards of care. Among surgeons, these measures are often over-looked. However, surgeons are at the forefront in preventing and managing infections. Surgeons are responsible for many of the processes of healthcare that impact the risk for surgical site infections and play a key role in their prevention. Surgeons are also at the forefront in managing patients with infections, who often need prompt source control and appropriate antibiotic therapy, and are directly responsible for their outcome. In this context, the direct leadership of surgeons in infection prevention and management is of utmost importance. In order to disseminate worldwide this message, the editorial has been translated into 9 different languages (Arabic, Chinese, French, German, Italian, Portuguese, Spanish, Russian, and Turkish).
  • Olkkola, Satu; Rossi, Mirko; Jaakkonen, Anniina; Simola, Maria; Tikkanen, Jouni; Hakkinen, Marjaana; Tuominen, Pirkko; Huitu, Otso; Niemimaa, Jukka; Henttonen, Heikki; Kivistö, Rauni (2021)
    Small mammals are known to carry Campylobacter spp.; however, little is known about the genotypes and their role in human infections. We studied intestinal content from small wild mammals collected in their natural habitats in Finland in 2010-2017, and in close proximity to 40 pig or cattle farms in 2017. The animals were trapped using traditional Finnish metal snap traps. Campylobacter spp. were isolated from the intestinal content using direct plating on mCCDA. A total of 19% of the captured wild animals (n = 577) and 41% of the pooled farm samples (n = 227) were positive for C. jejuni, which was the only Campylobacter species identified. The highest prevalence occurred in yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) which carried Campylobacter spp. in 66.3 and 63.9% of the farm samples and 41.5 and 24.4% of individual animals trapped from natural habitats, respectively. Interestingly, all house mouse (Mus musculus) and shrew (Sorex spp.) samples were negative for Campylobacter spp. C. jejuni isolates (n = 145) were further characterized by whole-genome sequencing. Core genome multilocus sequence typing (cgMLST) clustering showed that mouse and vole strains were separated from the rest of the C. jejuni population (636 and 671 allelic differences, 94 and 99% of core loci, respectively). Very little or no alleles were shared with C. jejuni genomes described earlier from livestock or human isolates. FastANI results further indicated that C. jejuni strains from voles are likely to represent a new previously undescribed species or subspecies of Campylobacter. Core-genome phylogeny showed that there was no difference between isolates originating from the farm and wild captured animals. Instead, the phylogeny followed the host species-association. There was some evidence (one strain each) of livestock-associated C. jejuni occurring in a farm-caught A. flavicollis and a brown rat (Rattus norvegicus), indicating that although small mammals may not be the original reservoir of Campylobacter colonizing livestock, they may sporadically carry C. jejuni strains occurring mainly in livestock and be associated with disease in humans.
  • Sartelli, Massimo; Labricciosa, Francesco M.; Coccolini, Federico; Coimbra, Raul; Abu-Zidan, Fikri M.; Ansaloni, Luca; Al-Hasan, Majdi N.; Ansari, Shamshul; Barie, Philip S.; Angel Cainzos, Miguel; Ceresoli, Marco; Chiarugi, Massimo; Claridge, Jeffrey A.; Cicuttin, Enrico; Dellinger, Evan Patchen; Fry, Donald E.; Guirao, Xavier; Hardcastle, Timothy Craig; Hecker, Andreas; Leppäniemi, Ari K.; Litvin, Andrey; Marwah, Sanjay; Maseda, Emilio; Mazuski, John E.; Memish, Ziad Ahmed; Kirkpatrick, Andrew W.; Pagani, Leonardo; Podda, Mauro; Rasa, Huseyin Kemal; Sakakushev, Boris E.; Sawyer, Robert G.; Tumietto, Fabio; Xiao, Yonghong; Aboubreeg, Wedad Faraj; Adamou, Harissou; Akhmeteli, Lali; Akin, Emrah; Alberio, Maria Grazia; Alconchel, Felipe; Magagi, Ibrahim Amadou; Arauz, Ana Belen; Argenio, Giulio; Atanasov, Boyko C.; Atici, Semra Demirli; Awad, Selmy Sabry; Baili, Efstratia; Bains, Lovenish; Bala, Miklosh; Baraket, Oussama; Baral, Suman; Belskii, Vladislav A.; Benboubker, Moussa; Ben-Ishay, Offir; Bordoni, Pierpaolo; Boumediene, Abdalia; Brisinda, Giuseppe; Cavazzuti, Laura; Chandy, Sujith J.; Chiarello, Maria Michela; Cillara, Nicola; Clarizia, Guglielmo; Cocuz, Maria-Elena; Cocuz, Iuliu Gabriel; Conti, Luigi; Coppola, Raffaella; Cui, Yunfeng; Czepiel, Jacek; D'Acapito, Fabrizio; Damaskos, Dimitrios; Das, Koray; De Simone, Belinda; Delibegovic, Samir; Demetrashvili, Zaza; Detanac, Dzemail S.; Dhingra, Sameer; Di Bella, Stefano; Dimitrov, Evgeni N.; Dogjani, Agron; D'Oria, Mario; Dumitru, Irina Magdalena; Elmangory, Mutasim M.; Enciu, Octavian; Fantoni, Massimo; Filipescu, Daniela; Fleres, Francesco; Foghetti, Domitilla; Fransvea, Pietro; Gachabayov, Mahir; Galeiras, Rita; Gattuso, Gianni; Ghannam, Wagih M.; Ghisetti, Valeria; Giraudo, Giorgio; Gonfa, Kebebe Bekele; Gonullu, Emre; Hamad, Yousif Tag Elsir Y.; Hecker, Matthias; Isik, Arda; Ismail, Nizar; Ismail, Azzain; Jain, Sumita Agarwal; Kanj, Souha S.; Kapoor, Garima; Karaiskos, Ilias; Kavalakat, Alfie J.; Kenig, Jakub; Khamis, Faryal; Khokha, Vladimir; Kiguba, Ronald; Kim, Jae Il; Kobe, Yoshiro; Kok, Kenneth Yuh Yen; Kovacevic, Bojan M.; Kryvoruchko, Igor Andreevich; Kuriyama, Akira; Landaluce-Olavarria, Aitor; Lasithiotakis, Konstantinos; Lohsiriwat, Varut; Lostoridis, Eftychios; Luppi, Davide; Vega, Gustavo Miguel Machain; Maegele, Marc; Marinis, Athanasios; Martines, Gennaro; Martinez-Perez, Aleix; Massalou, Damien; Mesina, Cristian; Metan, Gokhan; Guadalupe Miranda-Novales, Maria; Mishra, Shyam Kumar; Mohamed, Mohaned Ibrahim Hussein; Mohamedahmed, Ali Yasen Y.; Mora-Guzman, Ismael; Mulita, Francesk; Musina, Ana-Maria; Navsaria, Pradeep H.; Negoi, Ionut; Nita, Gabriela Elisa; O'Connor, Donal B.; Alberto Ordonez, Carlos; Pantalone, Desire; Panyko, Arpad; Papadopoulos, Aristeidis; Pararas, Nikolaos; Pata, Francesco; Patel, Tapan; Pellino, Gianluca; Perra, Teresa; Perrone, Gennaro; Pesce, Antonio; Pintar, Tadeja; Popivanov, Georgi Ivanov; Porcu, Alberto; Quiodettis, Martha Alexa; Rahim, Razrim; Mitul, Ashrarur Rahman; Reichert, Martin; Rems, Miran; Reynolds Campbell, Glendee Yolande; Rocha-Pereira, Nuno; Rodrigues, Gabriel; Roncancio Villamil, Gustavo Eduardo; Rossi, Stefano; Sall, Ibrahima; Kafil, Hossein Samadi; Sasia, Diego; Seni, Jeremiah; Seretis, Charalampos; Serradilla-Martin, Mario; Shelat, Vishal G.; Siribumrungwong, Boonying; Slavchev, Mihail; Solaini, Leonardo; Tan, Boun Kim; Tarasconi, Antonio; Tartaglia, Dario; Toma, Elena Adelina; Tomadze, Gia; Toro, Adriana; Tovani-Palone, Marcos Roberto; van Goor, Harry; Vasilescu, Alin; Vereczkei, Andras; Veroux, Massimiliano; Alberto Weckmann, Sergio; Widmer, Lukas Werner; Yahya, AliIbrahim; Zachariah, Sanoop K.; Zakaria, Andee Dzulkarnaen; Zubareva, Nadezhda; Zuidema, Wietse P.; Di Carlo, Isidoro; Cortese, Francesco; Baiocchi, Gian Luca; Maier, Ronald; Catena, Fausto (2022)
    Background The objectives of the study were to investigate the organizational characteristics of acute care facilities worldwide in preventing and managing infections in surgery; assess participants' perception regarding infection prevention and control (IPC) measures, antibiotic prescribing practices, and source control; describe awareness about the global burden of antimicrobial resistance (AMR) and IPC measures; and determine the role of the Coronavirus Disease 2019 pandemic on said awareness. Methods A cross-sectional web-based survey was conducted contacting 1432 health care workers (HCWs) belonging to a mailing list provided by the Global Alliance for Infections in Surgery. The self-administered questionnaire was developed by a multidisciplinary team. The survey was open from May 22, 2021, and June 22, 2021. Three reminders were sent, after 7, 14, and 21 days. Results Three hundred four respondents from 72 countries returned a questionnaire, with an overall response rate of 21.2%. Respectively, 90.4% and 68.8% of participants stated their hospital had a multidisciplinary IPC team or a multidisciplinary antimicrobial stewardship team. Local protocols for antimicrobial therapy of surgical infections and protocols for surgical antibiotic prophylaxis were present in 76.6% and 90.8% of hospitals, respectively. In 23.4% and 24.0% of hospitals no surveillance systems for surgical site infections and no monitoring systems of used antimicrobials were implemented. Patient and family involvement in IPC management was considered to be slightly or not important in their hospital by the majority of respondents (65.1%). Awareness of the global burden of AMR among HCWs was considered very important or important by 54.6% of participants. The COVID-19 pandemic was considered by 80.3% of respondents as a very important or important factor in raising HCWs awareness of the IPC programs in their hospital. Based on the survey results, the authors developed 15 statements for several questions regarding the prevention and management of infections in surgery. The statements may be the starting point for designing future evidence-based recommendations. Conclusion Adequacy of prevention and management of infections in acute care facilities depends on HCWs behaviours and on the organizational characteristics of acute health care facilities to support best practices and promote behavioural change. Patient involvement in the implementation of IPC is still little considered. A debate on how operationalising a fundamental change to IPC, from being solely the HCWs responsibility to one that involves a collaborative relationship between HCWs and patients, should be opened.
  • Suzuki, Satoru; Nakanishi, Sayoko; Tamminen, Manu; Yokokawa, Taichi; Sato-Takabe, Yuki; Ohta, Kohei; Chou, Hsin-Yiu; Muziasari, Windi I.; Virta, Marko (2019)
    The use of antibiotics in aquaculture causes selection pressure for antibiotic-resistant bacteria (ARB). Antibiotic resistance genes (ARGs) may persist in ARB and the environment for long time even after stopping drug administration. Here we show monthly differences in the occurrences of genes conferring resistance to sulfonamides (i.e. sul1, sul2, sul3), and tetracyclines (tet(M)) in Japanese aquaculture seawater accompanied by records of drug administration. sul2 was found to persist throughout the year, whereas the occurrences of sul1, sul3, and tet(M) changed month-to-month. sul3 and tet(M) were detected in natural bacterial assemblages in May and July, but not in colony-forming bacteria, thus suggesting that the sul3 was harbored by the non-culturable fraction of the bacterial community. Comparison of results from Taiwanese, Japanese, and Finnish aquaculture waters reveals that the profile of sul genes and tet(M) in Taiwan resembles that in Japan, but is distinct from that in Finland. To our knowledge, this work represents the first report to use the same method to compare the dynamics of sul genes and tet(M) in aquaculture seawater in different countries. (C) 2019 Elsevier B.V. All rights reserved.
  • Kovanen, Sara; Rossi, Mirko; Pohja-Mykrä, Mari; Nieminen, Timo; Raunio-Saarnisto, Mirja; Sauvala, Mikaela; Fredriksson-Ahomaa, Maria; Hänninen, Marja-Liisa; Kivistö, Rauni Inari (2019)
    Poultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized Campylobacter jejuni from western jackdaws (n = 91, 43%), mallard ducks (n = 82, 76%), and pheasants (n = 9, 9%). Most of the western jackdaw and mallard duck C. jejuni isolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdaw C. jejuni isolates, e.g., a novel cdtABC gene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention. IMPORTANCE The roles of environmental reservoirs, including wild birds, in the molecular epidemiology of Campylobacter jejuni have not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they had C. jejuni genomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships of C. jejuni isolates.
  • Karkman, Antti; Berglund, Fanny; Flach, Carl-Fredrik; Kristiansson, Erik; Larsson, D. G. Joakim (2020)
    Antibiotic resistance surveillance through regional and up-to-date testing of clinical isolates is a foundation for implementing effective empirical treatment. Surveillance data also provides an overview of geographical and temporal changes that are invaluable for guiding interventions. Still, due to limited infrastructure and resources, clinical surveillance data is lacking in many parts of the world. Given that sewage is largely made up of human fecal bacteria from many people, sewage epidemiology could provide a cost-efficient strategy to partly fill the current gap in clinical surveillance of antibiotic resistance. Here we explored the potential of sewage metagenomic data to assess clinical antibiotic resistance prevalence using environmental and clinical surveillance data from across the world. The sewage resistome correlated to clinical surveillance data of invasive Escherichia coli isolates, but none of several tested approaches provided a sufficient resolution for clear discrimination between resistance towards different classes of antibiotics. However, in combination with socioeconomic data, the overall clinical resistance situation could be predicted with good precision. We conclude that analyses of bacterial genes in sewage could contribute to informing management of antibiotic resistance. Karkman et al. explore how well available global sewage metagenomic data can predict clinical resistance prevalence using different models. A combination of sewage metagenomic data with socioeconomic factors predicts overall clinical resistance well, but still has limited ability to discriminate between resistance to different classes of antibiotics.
  • Hiitiö, Heidi; Vakkamäki, Johanna; Simojoki, Heli; Autio, Tiina; Junnila, Jouni; Pelkonen, Sinikka; Pyörälä, Satu (2017)
    Background: The dairy industry has undergone substantial structural changes as intensive farming has developed during recent decades. Mastitis continues to be the most common production disease of dairy cows. Nationwide surveys of mastitis prevalence are useful in monitoring udder health of dairy herds and to study the impact of structural changes on the dairy industry. This survey on bovine subclinical mastitis was the first based on cow composite milk somatic cell count (SCC) data from the Finnish national health monitoring and milk recording database. A cow with composite milk SCC = 200,000 cells/ml in at least one of the four test milkings during the year was considered to have subclinical mastitis and a cow with composite milk SCC = 200,000 cells/ml in three or in all four test milkings during the year to have chronic subclinical mastitis. The aim of the study was to determine the prevalence of subclinical mastitis and chronic subclinical mastitis in Finland in 1991, 2001 and 2010 and to investigate cow and herd factors associated with elevated SCC. Results: Prevalence of subclinical mastitis in Finland decreased over recent decades from 22.3% (1991) and 20.1% (2001) to 19.0% (2010). Prevalence of chronic subclinical mastitis was 20.4% in 1991, 15.5% in 2001 and 16.1% in 2010. The most significant cow and herd factors associated with subclinical mastitis or high milk SCC were increasing parity, Holstein breed, free- stalls with an automatic milking system and organic production. Milk SCC were highest from July to September. Main factors associated with chronic mastitis were increasing parity and Holstein breed. Conclusions: Prevalence of subclinical mastitis in Finland decreased over recent decades, the greatest change taking place during the first decade of the study. Prevalence of chronic subclinical mastitis significantly decreased from 1991. The most significant factors associated with both types of mastitis were increasing parity and Holstein breed, and for subclinical mastitis also free-stalls with automatic milking. National surveys on mastitis prevalence should be carried out at regular intervals to monitor udder health of dairy cows and to study the impact of the ongoing structural changes in the dairy industry to enable interventions related to udder health to be made when needed.