Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond

publishedVersio

Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond

publishedVersio

Small-Scale Comparative Genomic Analysis of Listeria monocytogenes Isolated from Environments of Salmon Processing Plants and Human Cases in Norway

Listeria monocytogenes is a food-borne bacterium that give rise to the potentially life-threatening disease listeriosis. Listeriosis has been mandatorily notifiable in Norway since 1991. All clinical L. monocytogenes isolates are sent to the Norwegian Institute of Public Health (NIPH) for typing. Since 2005 Multi-Locus Variable number tandem repeats Analysis (MLVA) has been used for typing but was recently replaced by whole genome sequencing using core genome Multi-Locus Sequence Typing (cgMLST). In the present study, L. monocytogenes isolates collected at salmon processing plants in Norway in 2007 (n = 12) and 2015 (n = 14) were first subject to MLVA. Twelve clinical L. monocytogenes isolates with matching MLVA profile and sampling time were selected from the strain collection at NIPH. Twenty-one isolates from the salmon processing plants and all clinical isolates (n = 12) were whole genome sequenced and compared using cgMLST and in silico detection of virulence genes. cgMLST revealed four pairs of environmental–human isolates with ≤10 allelic differences over 1708 genes, indicating that they may be assigned as clonal, with the implication that they are descended from the same recent ancestor. No relevant difference in carriage of virulence genes was found between environmental or human isolates. The present study shows that L. monocytogenes strains that genetically resemble contemporary isolates from human listeriosis circulate in Norwegian salmon slaughterhouses, and carry the same virulence genes

Implications of stx loss for clinical diagnostics of Shiga toxin-producing Escherichia coli

The dynamics related to the loss of stx genes from Shiga toxin-producing Escherichia coli remain unclear. Current diagnostic procedures have shortcomings in the detection and identification of STEC. This is partly owing to the fact that stx genes may be lost during an infection or in the laboratory. The aim of the present study was to provide new insight into in vivo and in vitro stx loss in order to improve diagnostic procedures. Results from the study support the theory that loss of stx is a strain-related phenomenon and not induced by patient factors. It was observed that one strain could lose stx both in vivo and in vitro. Whole genome comparison of stx-positive and stx-negative isolates from the same patient revealed that different genomic rearrangements, such as complete or partial loss of the parent prophage, may be factors in the loss of stx. Of diagnostic interest, it was shown that patients can be co-infected with different E. coli pathotypes. Therefore, identification of eae-positive, but stx-negative isolates should not be interpreted as “Shiga toxin-lost” E. coli without further testing. Growth and recovery of STEC were supported by different selective agar media for different strains, arguing for inclusion of several media in STEC diagnostics

Small-Scale Comparative Genomic Analysis of Listeria monocytogenes Isolated from Environments of Salmon Processing Plants and Human Cases in Norway

Listeria monocytogenes is a food-borne bacterium that give rise to the potentially life-threatening disease listeriosis. Listeriosis has been mandatorily notifiable in Norway since 1991. All clinical L. monocytogenes isolates are sent to the Norwegian Institute of Public Health (NIPH) for typing. Since 2005 Multi-Locus Variable number tandem repeats Analysis (MLVA) has been used for typing but was recently replaced by whole genome sequencing using core genome Multi-Locus Sequence Typing (cgMLST). In the present study, L. monocytogenes isolates collected at salmon processing plants in Norway in 2007 (n = 12) and 2015 (n = 14) were first subject to MLVA. Twelve clinical L. monocytogenes isolates with matching MLVA profile and sampling time were selected from the strain collection at NIPH. Twenty-one isolates from the salmon processing plants and all clinical isolates (n = 12) were whole genome sequenced and compared using cgMLST and in silico detection of virulence genes. cgMLST revealed four pairs of environmental–human isolates with ≤10 allelic differences over 1708 genes, indicating that they may be assigned as clonal, with the implication that they are descended from the same recent ancestor. No relevant difference in carriage of virulence genes was found between environmental or human isolates. The present study shows that L. monocytogenes strains that genetically resemble contemporary isolates from human listeriosis circulate in Norwegian salmon slaughterhouses, and carry the same virulence genes

Small-Scale Comparative Genomic Analysis of Listeria monocytogenes Isolated from Environments of Salmon Processing Plants and Human Cases in Norway

Listeria monocytogenes is a food-borne bacterium that give rise to the potentially life-threatening disease listeriosis. Listeriosis has been mandatorily notifiable in Norway since 1991. All clinical L. monocytogenes isolates are sent to the Norwegian Institute of Public Health (NIPH) for typing. Since 2005 Multi-Locus Variable number tandem repeats Analysis (MLVA) has been used for typing but was recently replaced by whole genome sequencing using core genome Multi-Locus Sequence Typing (cgMLST). In the present study, L. monocytogenes isolates collected at salmon processing plants in Norway in 2007 (n = 12) and 2015 (n = 14) were first subject to MLVA. Twelve clinical L. monocytogenes isolates with matching MLVA profile and sampling time were selected from the strain collection at NIPH. Twenty-one isolates from the salmon processing plants and all clinical isolates (n = 12) were whole genome sequenced and compared using cgMLST and in silico detection of virulence genes. cgMLST revealed four pairs of environmental–human isolates with ≤10 allelic differences over 1708 genes, indicating that they may be assigned as clonal, with the implication that they are descended from the same recent ancestor. No relevant difference in carriage of virulence genes was found between environmental or human isolates. The present study shows that L. monocytogenes strains that genetically resemble contemporary isolates from human listeriosis circulate in Norwegian salmon slaughterhouses, and carry the same virulence genes.publishedVersio

Small-Scale Comparative Genomic Analysis of Listeria monocytogenes Isolated from Environments of Salmon Processing Plants and Human Cases in Norway

Listeria monocytogenes is a food-borne bacterium that give rise to the potentially life-threatening disease listeriosis. Listeriosis has been mandatorily notifiable in Norway since 1991. All clinical L. monocytogenes isolates are sent to the Norwegian Institute of Public Health (NIPH) for typing. Since 2005 Multi-Locus Variable number tandem repeats Analysis (MLVA) has been used for typing but was recently replaced by whole genome sequencing using core genome Multi-Locus Sequence Typing (cgMLST). In the present study, L. monocytogenes isolates collected at salmon processing plants in Norway in 2007 (n = 12) and 2015 (n = 14) were first subject to MLVA. Twelve clinical L. monocytogenes isolates with matching MLVA profile and sampling time were selected from the strain collection at NIPH. Twenty-one isolates from the salmon processing plants and all clinical isolates (n = 12) were whole genome sequenced and compared using cgMLST and in silico detection of virulence genes. cgMLST revealed four pairs of environmental–human isolates with ≤10 allelic differences over 1708 genes, indicating that they may be assigned as clonal, with the implication that they are descended from the same recent ancestor. No relevant difference in carriage of virulence genes was found between environmental or human isolates. The present study shows that L. monocytogenes strains that genetically resemble contemporary isolates from human listeriosis circulate in Norwegian salmon slaughterhouses, and carry the same virulence genes

Implementation of multiplex PCR diagnostics for gastrointestinal pathogens linked to increase of notified Shiga toxin-producing Escherichia coli cases in Norway, 2007?2017

The aim of this study was to investigate implementation of multiplex PCR assays (broad screening PCR) on the distribution and characteristics of notified Shiga toxin-producing Escherichia coli (STEC) cases in Norway, 2007–2017. We described STEC cases notified to the Norwegian Surveillance System for Communicable Diseases (MSIS), 2007–2017 and categorised cases as high-virulent, low-virulent or unclassifiable STEC infections based on guidelines for follow-up of STEC cases. We conducted descriptive analysis and time series analysis allowing for trends and seasonality, and calculated adjusted incidence rate ratios (aIRR) using negative binomial regression for laboratories with and without broad screening PCR. A total of 1458 STEC cases were notified to MSIS (2007–2017), median age 21 years, 51% female. Cases were categorised as having 475 (33%) high-virulent, 652 (45%) low-virulent, and 331 (23%) unclassifiable STEC infections. We observed a higher increasing monthly trend in cases (aIRR = 1.020; 95% CI 1.016–1.024) notified from laboratories with broad screening PCR (n = 4) compared to laboratories (n = 17) without (aIRR = 1.011; 95% CI 1.007–1.014). Notification of low-virulent STEC infections increased from laboratories with broad screening PCR. The increase in notified STEC cases was prominent in cases categorised with a low-virulent STEC infection and largely attributable to unselective screening methods. We recommend NIPH to maintain differentiated control measures for STEC cases to avoid follow-up of low-virulent STEC infections. We recommend microbiological laboratories in Norway to consider a more cost-effective broad screening PCR strategy that enables differentiation of high-virulent STEC infections