Detection of VIM-1-producing Enterobacter cloacae and Salmonella enterica Serovars Infantis and Goldcoast at a breeding pig farm in Germany in 2017 and their molecular relationship to former VIM-1-producing S. Infantis Isolates in German livestock production

In 2011, VIM-1-producing Salmonella enterica serovar Infantis and Escherichia coli were isolated for the first time in four German livestock farms. In 2015/2016, highly related isolates were identified in German pig production. This raised the issue of potential reservoirs for these isolates, the relation of their mobile genetic elements, and potential links between the different affected farms/facilities. In a piglet-producing farm suspicious for being linked to some blaVIM-1 findings in Germany, fecal and environmental samples were examined for the presence of carbapenemase-producing Enterobacteriaceae and Salmonella spp. Newly discovered isolates were subjected to Illumina whole-genome sequencing (WGS) and S1 pulsed-field gel electrophoresis (PFGE) hybridization experiments. WGS data of these isolates were compared with those for the previously isolated VIM-1-producing Salmonella Infantis isolates from pigs and poultry. Among 103 samples, one Salmonella Goldcoast isolate, one Salmonella Infantis isolate, and one Enterobacter cloacae isolate carrying the blaVIM-1 gene were detected. Comparative WGS analysis revealed that the blaVIM-1 gene was part of a particular Tn21-like transposable element in all isolates. It was located on IncHI2 (ST1) plasmids of ∼290 to 300 kb with a backbone highly similar (98 to 100%) to that of reference pSE15-SA01028. SNP analysis revealed a close relationship of all VIM-1-positive S. Infantis isolates described since 2011. The findings of this study demonstrate that the occurrence of the blaVIM-1 gene in German livestock is restricted neither to a certain bacterial species nor to a certain Salmonella serovar but is linked to a particular Tn21-like transposable element located on transferable pSE15-SA01028-like IncHI2 (ST1) plasmids, being present in all of the investigated isolates from 2011 to 2017. IMPORTANCE: Carbapenems are considered one of few remaining treatment options against multidrug-resistant Gram-negative pathogens in human clinical settings. The occurrence of carbapenemase-producing Enterobacteriaceae in livestock and food is a major public health concern. Particularly the occurrence of VIM-1-producing Salmonella Infantis in livestock farms is worrisome, as this zoonotic pathogen is one of the main causes for human salmonellosis in Europe. Investigations on the epidemiology of those carbapenemase-producing isolates and associated mobile genetic elements through an in-depth molecular characterization are indispensable to understand the transmission of carbapenemase-producing Enterobacteriaceae along the food chain and between different populations to develop strategies to prevent their further spread

Die Übertragung und strukturelle Veränderung der Carbapenemasegen-tragende Plasmide im Tiermodell Huhn

The antimicrobial resistance remains an important threat to the public and animal health. The current trends of antimicrobial resistance reveal an alarming and ongoing dissemination of associated genes to different bacteria. With the aim of preserving important antimicrobials for human treatment, certain antimicrobial classes, such as carbapenems are categorized as critically important antimicrobials and are not licensed for use in foodproducing animals. However, in recent years, reports of carbapenemase-producing bacteria in livestock animals started to emerge. In Germany, several studies reported detection of carbapenemase-producing enterobacteria in wild birds, livestock, meat and seafood products. An important observation was association of New Delhi Metallo (NDM-1) and Verona Integron Metallo (VIM-1) carbapenemases to different Salmonella serovars, suggesting their role as reservoirs of these carbapenemases. Motivated by the detection of carbapenemase-producing Salmonella serovars in a wild bird and poultry production, in this doctoral thesis scenarios of avian native NDM-1-producing Salmonella enterica subsp. enterica serovar (S.) Corvallis and VIM-1-producing S. Infantis entering a broiler flock were investigated. The aim of the in vivo studies was to understand behavior of these strains and their plasmids in the absence of antibiotic pressure. Particular focus was on the in vivo spread and stability of carbapenemase-encoding blaNDM-1-carrying plasmids belonging to the incompatibility group A/C2 (IncA/C2) and blaVIM-1-carrying plasmids belonging to group HI2 (IncHI2). The insight into transfer and structural alteration of plasmids was obtained by an in-depth molecular analysis with S1-pulsed-field gel electrophoresis plasmid profiling and subsequent short and long-read whole genome sequencing analysis. The in vivo studies showed that in a scenario of NDM-1-producing S. Corvallis entering a broiler flock, the blaNDM-1-carrying IncA/C2 plasmid disseminates to different gut enterobacteria, such as Escherichia (E.) coli and Klebsiella (K.) pneumoniae, in the absence of antibiotic pressure. The acquisition of this plasmid was not restricted to a particular E. coli clone, as this plasmid was detected in different E. coli ST-types and a K. pneumoniae strain. The blaNDM-1-carrying IncA/C2 plasmid remained detected in donor and E. coli strains until the end of trial, revealing stable persistence of this plasmid also in new hosts. Although less frequent in contrast to gut enterobacteria, acquisition of the blaNDM-1-carrying IncA/C2 plasmid in broiler-associated S. Paratyphi B (dTartrate-positive) and S. Infantis strains was detected. Acquisition of the blaVIM-1-carrying IncHI2 plasmid was not detected in other bacteria during the course of in vivo study. As for the in vivo stability of blaNDM-1-carrying IncA/C2 and blaVIM-1-carrying IncHI2 plasmid, stable persistence of these plasmids in their native hosts was observed. In the case of blaNDM-1-carrying IncA/C2 plasmid a smaller (~10 kb) and larger (~70 kb) structural deletion was identified, along with formation of a newly emerged blaNDM-1-carrying IncA/C2-IncHI2 multireplicon megaplasmid. Despite structural alterations, the blaNDM-1 gene was maintained in these variants of the blaNDM-1-carrying IncA/C2 plasmid. In the selection of blaVIM-1-carrying IncHI2 plasmids, from donor reisolates, smaller (~10 kb) structural deletions were observed. In conclusion, the in vivo broiler chicken infection studies revealed stable persistence of the blaNDM-1-carrying IncA/C2 and blaVIM-1-carrying IncHI2 plasmids, despite sporadic structural alterations, in their hosts in a scenario of entry into a broiler flock. As for blaNDM-1-carrying IncA/C2 plasmid, a worrying observation is the rapid and broad dissemination of the blaNDM-1-carrying IncA/C2 plasmid to gut enterobacteria and Salmonella recipients in the absence of selective pressure. Although here primarily investigating the behavior of NDM-1-producing S. Corvallis and VIM-1-producing S. Infantis strains, the results can serve as a model for the potential dissemination of other MDR-encoding broad host range plasmids in a broiler flock. Therefore, important preventive measure should be achieved to avoid such bacteria entering a broiler flock, as their entrance could lead to the spread of MDR-encoding plasmids even in the absence of antibiotic pressure.Die Antibiotikaresistenzen stellen nach wie vor eine große Bedrohung für die Gesundheit von Menschen und Tieren dar. Die derzeitigen Entwicklungen der Antibiotikaresistenzen zeigen eine alarmierende und anhaltende Verbreitung der Antibiotikaresistenzgene bei verschiedenen Bakterien. Mit dem Ziel, die wichtigsten Antibiotika für die Behandlung von Menschen zu bewahren, werden bestimmten Gruppen von Antibiotika, wie z.B. Carbapenemen, als Reserveantibiotika eingestuft und dürfen bei Nutzieren nicht verwendet werden. In den letzten Jahren wurden dennoch Carbapenemaseproduzierende Bakterien bei Nutztieren isoliert. In Deutschland haben mehrere Studien über den Nachweis von Carbapenemase-produzierende Enterobakterien in Wildvögeln, Nutztieren, Fleisch und Meeresfrüchten berichtet. Eine wichtige Beobachtung dieser Studien war der Zusammenhang der New Delhi Metallo (NDM-1) und Verona Integron Metallo (VIM-1) Carbapenemasen mit unterschiedlichen Salmonellen, was darauf hindeutet, dass die Salmonellen mögliche Reservoire dieser Carbapenemasen sind. Motiviert durch den Nachweis von Carbapenemase-produzierenden Salmonellen bei einem Wildvogel und in der Geflügelproduktion wurden in dieser Dissertation Eintrittsszenarien einer aviären NDM-1-produzierenden Salmonella enterica subsp. enterica serovar (S.) Corvallis und einer VIM-1-produzierenden S. Infantis in einen Masthähnchenbestand untersucht. In den in vivo Studien wurde das Verhalten dieser Salmonellen und der dazugehörigen Plasmide ohne Antibiotika-Einsatz untersucht. Insbesondere wurden hier die in vivo Übertragung und die Stabilität der Carbapenemasekodierenden blaNDM-1-tragenden Plasmide der Inkompatibilitätsgruppe A/C2 (IncA/C2) und blaVIM-1-tragenden Plasmide der Inkompatibilitätsgruppe HI2 (IncHI2) untersucht. Der Einblick in der Verbreitung und die Stabilität der Plasmide wurde durch die Verwendung von molekularbiologischen Methoden S1-Puls-Feld-Gelelektrophorese und die Gesamtgenomsequenzierung ermöglicht. Die in vivo Studien haben gezeigt, dass in einem Szenario in dem der NDM-1-produzierende S. Corvallis in einen Masthähnchenbestand eintritt, das blaNDM-1-tragende IncA/C2 Plasmid sich in unterschiedlichen Darmenterobakterien wie Escherichia (E.) coli und Klebsiella (K.) pneumoniae auch ohne Antibiotika-Einsatz verbreiten kann. Die Verbreitung dieses Plasmids war nicht auf einen bestimmten E. coli-Klon beschränkt. Das Plasmid wurde in verschiedenen E. coli ST-Typen und einem K. pneumoniae-Stamm nachgewiesen. Das blaNDM-1-tragende IncA/C2 Plasmid konnte in den Donorzellen und E. coli-Stämmen bis Ende des Versuchs nachgewiesen werden, was für eine stabile Persistenz des Plasmids in anderen Bakterien spricht. Im Gegensatz zu Darmenterobakterien war die Aufnahme des blaNDM-1-tragenden IncA/C2-Plasmids in Broiler-assoziierten S. Paratyphi B (dTartrat-positiv) und S. Infantis weniger häufig. Die Aufnahme des blaVIM-1-tragenden IncHI2 Plasmids in anderen Bakterien konnte im Verlauf der in vivo Studie nicht nachgewiesen werden. Bezüglich der in vivo Stabilität der blaNDM-1-tragenden IncA/C2 und blaVIM-1-tragenden IncHI2 Plasmide wurde eine stabile Persistenz dieser Plasmide in ihren Donorzellen beobachtet. Bei den blaNDM-1-tragenden IncA/C2 Plasmiden wurde eine kleinere (~10 kb) und eine größere (~70 kb) Deletion in dem Plasmid sowie die Entsehung eines blaNDM-1-tragenden IncA/C2-IncHI2-Multireplikon-Megaplasmids beobachtet. Trotz strukturellen Veränderungen des Plasmids konnte das blaNDM-1 Gen in diesen Varianten des blaNDM-1-tragenden IncA/C2 Plasmids nachgewiesen werden. Bei den untersuchten blaVIM-1-tragenden IncHI2 Plasmiden wurden kleinere (~10 kb) Deletionen beobachtet. Die im Tiermodell Huhn durchgeführten in vivo Studien haben eine stabile Persistenz der blaNDM-1-tragenden IncA/C2 und blaVIM-1-tragenden IncHI2-Plasmide in Donorzellen bei einem Eintrittsszenario in einen Masthähnchenbestand gezeigt. Besorgniserregend ist die Verbreitung des blaNDM-1-tragenden IncA/C2 Plasmids zu den Darmenterobakterien und Salmonellen ohne Antibiotika-Einsatz. Obwohl in den dargestellten Studien das Verhalten der NDM-1-produzierenden S. Corvallis und VIM-1-produzierenden S. Infantis untersucht wurde, können die Ergebnisse dennoch als ein Modell für die Verbreitung von Multiresistenzkodierenden Plasmiden in einem Masthänchenbestand dienen. Somit sollten Präventivmaßnahmen ergriffen werden um den Eintritt solcher Bakterien in einen Masthänchenbestand zu verhindern, insbesondere weil ihr Eintritt zur Verbreitung von Multiresistenz-kodierenden Plasmiden auch ohne Antibiotika-Einsatz führen könnte

Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017

In spring 2016, Greece reported an outbreak caused by a previously undescribed Salmonellaenterica subsp. enterica serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presumptive vehicle. Subsequently, Germany, Czech Republic, Luxembourg and the United Kingdom (UK) reported infections with this novel serotype via EPIS-FWD. Concerned countries in collaboration with the European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA) adopted a common outbreak case definition. An outbreak case was defined as a laboratory-confirmed notification of the novel Salmonella serotype. Between March 2016 and April 2017, 47 outbreak cases were notified (Greece: n = 22; Germany: n = 13; Czech Republic: n = 5; Luxembourg: n = 4; UK: n = 3). Whole genome sequencing revealed the very close genetic relatedness of isolates from all affected countries. Interviews focusing on sesame product consumption, suspicious food item testing and trace-back analysis following Salmonella spp. detection in food products identified a company in Greece where sesame seeds from different countries were processed. Through European collaboration, it was possible to identify and recall sesame spread as one contaminated food item serving as vehicle of infection and trace it back to its origin.Peer Reviewe

Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017

In spring 2016, Greece reported an outbreak caused by a previously undescribed Salmonella enterica subsp. enterica serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food-and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presumptive vehicle. Subsequently, Germany, Czech Republic, Luxembourg and the United Kingdom (UK) reported infections with this novel serotype via EPIS-FWD. Concerned countries in collaboration with the European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA) adopted a common outbreak case definition. An outbreak case was defined as a laboratory-confirmed notification of the novel Salmonella serotype. Between March 2016 and April 2017, 47 outbreak cases were notified (Greece: n = 22; Germany: n = 13; Czech Republic: n = 5; Luxembourg: n = 4; UK: n = 3). Whole genome sequencing revealed the very close genetic relatedness of isolates from all affected countries. Interviews focusing on sesame product consumption, suspicious food item testing and trace-back analysis following Salmonella spp. detection in food products identified a company in Greece where sesame seeds from different countries were processed. Through European collaboration, it was possible to identify and recall sesame spread as one contaminated food item serving as vehicle of infection and trace it back to its origin