An appeal for strengthening genomic pathogen surveillance to improve pandemic preparedness and infection prevention: the German perspective

The SARS-CoV-2 pandemic has highlighted the importance of viable infection surveillance and the relevant infrastructure. From a German perspective, an integral part of this infrastructure, genomic pathogen sequencing, was at best fragmentary and stretched to its limits due to the lack or inefficient use of equipment, human resources, data management and coordination. The experience in other countries has shown that the rate of sequenced positive samples and linkage of genomic and epidemiological data (person, place, time) represent important factors for a successful application of genomic pathogen surveillance. Planning, establishing and consistently supporting adequate structures for genomic pathogen surveillance will be crucial to identify and combat future pandemics as well as other challenges in infectious diseases such as multi-drug resistant bacteria and healthcare-associated infections. Therefore, the authors propose a multifaceted and coordinated process for the definition of procedural, legal and technical standards for comprehensive genomic pathogen surveillance in Germany, covering the areas of genomic sequencing, data collection and data linkage, as well as target pathogens. A comparative analysis of the structures established in Germany and in other countries is applied. This proposal aims to better tackle epi- and pandemics to come and take action from the “lessons learned” from the SARS-CoV-2 pandemic

Molecular typing of ST239-MRSA-III from diverse geographic locations and the evolution of the SCCmec III element during its intercontinental spread

ST239-MRSA-III is probably the oldest truly pandemic MRSA strain, circulating in many countries since the 1970s. It is still frequently isolated in some parts of the world although it has been replaced by other MRSA strains in, e.g., most of Europe. Previous genotyping work (Harris et al., 2010; Castillo-Ramírez et al., 2012) suggested a split in geographically defined clades. In the present study, a collection of 184 ST239-MRSA-III isolates, mainly from countries not covered by the previous studies were characterized using two DNA microarrays (i) targeting an extensive range of typing markers, virulence and resistance genes and (ii) a SCCmec subtyping array. Thirty additional isolates underwent whole-genome sequencing (WGS) and, together with published WGS data for 215 ST239-MRSA-III isolates, were analyzed using in-silico analysis for comparison with the microarray data and with special regard to variation within SCCmec elements. This permitted the assignment of isolates and sequences to 39 different SCCmec III subtypes, and to three major and several minor clades. One clade, characterized by the integration of a transposon into nsaB and by the loss of fnbB and splE was detected among isolates from Turkey, Romania and other Eastern European countries, Russia, Pakistan, and (mainly Northern) China. Another clade, harboring sasX/sesI is widespread in South-East Asia including China/Hong Kong, and surprisingly also in Trinidad & Tobago. A third, related, but sasX/sesI-negative clade occurs not only in Latin America but also in Russia and in the Middle East from where it apparently originated and from where it also was transferred to Ireland. Minor clades exist or existed in Western Europe and Greece, in Portugal, in Australia and New Zealand as well as in the Middle East. Isolates from countries where this strain is not epidemic (such as Germany) frequently are associated with foreign travel and/or hospitalization abroad. The wide dissemination of this strain and the fact that it was able to cause a hospital-borne pandemic that lasted nearly 50 years emphasizes the need for stringent infection prevention and control and admission screening

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

First Insights into the Genome Sequence of Pseudomonas oleovorans DSM 1045

The Gram-negative proteobacterium Pseudomonas oleovorans DSM 1045 is considered a promising source for enzymes of biotechnological interest, e.g., hydrolases and transaminases. Here, we present a draft sequence of its 4.86-Mb genome, enabling the identification of novel biocatalysts

Neonatal and young infant sepsis by Group B Streptococci and Escherichia coli: a single-center retrospective analysis in Germany—GBS screening implementation gaps and reduction in antibiotic resistance

The last nationwide surveillance study on neonatal and young infant sepsis due to Group B Streptococci (GBS) and Escherichia coli in Germany was conducted between 2009 and 2010. The aim of this study is to provide longitudinal epidemiological data on neonatal and young infant sepsis caused by GBS and E. coli to reevaluate existing data and to inform clinical decision-making. Every positive blood culture for GBS and E. coli within the first 90 days of life that occurred at our center from 2008 until 2018 was identified. The epidemiological, clinical, laboratory, and microbiological data of all affected patients were analyzed through retrospective chart review, along with the pathogen's antimicrobial susceptibility results. In total, 106 episodes of neonatal sepsis were described; 31% (n = 33) being caused by GBS and 69% (n = 73) by E. coli; 87% of GBS early-onset disease (EOD) cases did not receive intrapartum antibiotic prophylaxis (IAP). Contrary to general trends, the proportion of resistant E. coli isolates decreased for all tested antibiotics over time. Coincidentally, antenatal antibiotic use beyond IAP during that period decreased significantly in our center.Conclusions: (1) Data at our center suggests at least a regional implementation gap in GBS screening and IAP. (2) The decline in the resistance rate of E. coli for all antimicrobial substances might indicate that the reduction of prenatal antibiotics use is beneficial and that neonatal antibiotic stewardship programs should include pregnant women as well. What is Known: • GBS screening and intrapartum antibiotic prophylaxis led to a 32%-reduction in GBS disease in Germany with a 0.75 (92:122) ratio of early-onset disease to late-onset disease in 2009-2010. • Prenatal antibiotic use might increase the risk of E. coli early-onset disease and antibiotic resistances. What is New: • The GBS early-onset disease rates were twice as high as those of late-onset disease, the ratio was 1.75 (21:12) in 2008-2018 at our institution. This suggests that there are at least regional implementation gaps in the antenatal GBS screening in Germany. • We found a decline in E. coli resistance rates over time for all antimicrobial substances. Reduction in use of prenatal antibiotics might be an explanation

Dissemination of high-level mupirocin-resistant CC22-MRSA-IV in Saxony

Mupirocin is used for eradicating methicillin-resistant (MRSA) in nasal colonization. A plasmid-borne gene, , is associated with high-level mupirocin resistance. Despite the fact that, among all MRSA from a tertiary care center in the German state of Saxony, the prevalence of , encoding high-level mupirocin resistance, was approximately 1% over a 15-year period from 2000–2015, a sharp increase to nearly 20% was observed in 2016/2017. DNA microarray profiling revealed that this was due to the dissemination of a variant of CC22-MRSA-IV (“Barnim Epidemic Strain” or “UK-EMRSA-15”), which, in addition to , harbors , , , and – in most isolates – (C). In order to prevent therapy failures and a further spread of this strain, the use of mupirocin should be more stringently controlled as well as guided by susceptibility testing. In addition, MRSA decolonization regimens that rely on other substances, such as betaisodona, polyhexanide or octenidine, should be considered

Rapid Identification of Carbapenemase Genes in Gram-Negative Bacteria with an Oligonucleotide Microarray-Based Assay

<div><p>Rapid molecular identification of carbapenemase genes in Gram-negative bacteria is crucial for infection control and prevention, surveillance and for epidemiological purposes. Furthermore, it may have a significant impact upon determining the appropriate initial treatment and greatly benefit for critically ill patients. A novel oligonucleotide microarray-based assay was developed to simultaneously detect genes encoding clinically important carbapenemases as well as selected extended (ESBL) and narrow spectrum (NSBL) beta-lactamases directly from clonal culture material within few hours. Additionally, a panel of species specific markers was included to identify <i>Escherichia coli</i>, <i>Pseudomonas aeruginosa</i>, <i>Citrobacter freundii/braakii</i>, <i>Klebsiella pneumoniae</i> and <i>Acinetobacter baumannii</i>. The assay was tested using a panel of 117 isolates collected from urinary, blood and stool samples. For these isolates, phenotypic identifications and susceptibility tests were available. An independent detection of carbapenemase, ESBL and NSBL genes was carried out by various external reference laboratories using PCR methods. In direct comparison, the microarray correctly identified 98.2% of the covered carbapenemase genes. This included <i>bla</i>VIM (13 out of 13), <i>bla</i>GIM (2/2), <i>bla</i>KPC (27/27), <i>bla</i>NDM (5/5), <i>bla</i>IMP-2/4/7/8/13/14/15/16/31 (10/10), <i>bla</i>OXA-23 (12/13), <i>bla</i>OXA-40-group (7/7), <i>bla</i>OXA-48-group (32/33), <i>bla</i>OXA-51 (1/1) and <i>bla</i>OXA-58 (1/1). Furthermore, the test correctly identified additional beta-lactamases [<i>bla</i>OXA-1 (16/16), <i>bla</i>OXA-2 (4/4), <i>bla</i>OXA-9 (33/33), OXA-10 (3/3), <i>bla</i>OXA-51 (25/25), <i>bla</i>OXA-58 (2/2), CTX-M1/M15 (17/17) and <i>bla</i>VIM (1/1)]. In direct comparison to phenotypical identification obtained by VITEK or MALDI-TOF systems, 114 of 117 (97.4%) isolates, including <i>Acinetobacter baumannii</i> (28/28), <i>Enterobacter spec</i>. (5/5), <i>Escherichia coli</i> (4/4), <i>Klebsiella pneumoniae</i> (62/63), <i>Klebsiella oxytoca</i> (0/2), <i>Pseudomonas aeruginosa</i> (12/12), <i>Citrobacter freundii</i> (1/1) and <i>Citrobacter braakii</i> (2/2), were correctly identified by a panel of species specific probes. This assay might be easily extended, adapted and transferred to point of care platforms enabling fast surveillance, rapid detection and appropriate early treatment of infections caused by multiresistant Gram-negative bacteria.</p></div

Species genotyping results of the <b>M</b>icroarray-based assay in comparison to the <b>R</b>eference method (phenotypic results were obtained from University Medical Center of Dresden, University Medical Center of Jena, German Collection of Microorganisms and Cell Cultures, Institut Pasteur and Friedrich-Loeffler-Institute).

<p>Species genotyping results of the <b><u>M</u></b>icroarray-based assay in comparison to the <b><u>R</u></b>eference method (phenotypic results were obtained from University Medical Center of Dresden, University Medical Center of Jena, German Collection of Microorganisms and Cell Cultures, Institut Pasteur and Friedrich-Loeffler-Institute).</p

Linear multiplex DNA amplification, labeling and hybridization with the ArrayStrips.

<p>(<b>a</b>) Linear Multiplex Amplification starting from clonal RNA-free genomic DNA. Extracted DNA is internally labeled with biotin (Label [L]) and amplified in a linear multiplex PCR reaction; (<b>b</b>) Hybridization: the internally biotin labeled, single-stranded DNA product hybridizes specifically under stringent conditions to the corresponding probes. The resulting duplex is detected using a horse-radish peroxidase (Enzyme [E]) – streptavidin conjugate, which causes the dye to precipitate ([S]). (<b>c</b>) Detection: the ArrayMate Reader (or ArrayTube Reader ATR 03) enables the visualization and subsequently automated analysis of the array image. The presence of a dark precipitated spot indicates successful hybridization; (<b>d</b>) Analysis: the assay specific software analysis script coming with the ArrayMate Reader (or ArrayTube Reader ATR 03), measures the signal intensity of each probe and determines which genes/alleles are present in the sample by means of an assay specific algorithm. (<b>e</b>) Genotype analysis: a software plugin coming with the ArrayMate Reader (or ArrayTube Reader ATR 03) analyzed the raw data automatically, finally a report is provided on the detected carbapenemases genes.</p

Additional lactamases detected by the microarray in comparison to conducted control PCRs.

<p>Additional lactamases detected by the microarray in comparison to conducted control PCRs.</p