Cryptic SARS-CoV-2 lineage identified on two mink farms as a possible result of long-term undetected circulation in an unknown animal reservoir, Poland, November 2022 to January 2023

In late 2022 and early 2023, SARS-CoV-2 infections were detected on three mink farms in Poland situated within a few km from each other. Whole-genome sequencing of the viruses on two of the farms showed that they were related to a virus identified in humans in the same region 2 years before (B.1.1.307 lineage). Many mutations were found, including in the S protein typical of adaptations to the mink host. The origin of the virus remains to be determined.</p

Gut resistome of NSCLC patients treated with immunotherapy

BackgroundThe newest method of treatment for patients with NSCLC (non-small cell lung cancer) is immunotherapy directed at the immune checkpoints PD-1 (Programmed Cell Death 1) and PD-L1 (Programmed Cell Death Ligand 1). PD-L1 is the only validated predictor factor for immunotherapy efficacy, but it is imperfect. Some patients do not benefit from immunotherapy and may develop primary or secondary resistance. This study aimed to assess the intestinal resistome composition of non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors in the context of clinical features and potentially new prediction factors for assessing immunotherapy efficacy.MethodsThe study included 30 advanced NSCLC patients, 19 (57%) men and 11 (33%) women treated with first- or second-line immunotherapy (nivolumab, pembrolizumab or atezolizumab). We evaluated the patient’s gut resistome composition using the high sensitivity of targeted metagenomics.ResultsStudies have shown that resistome richness is associated with clinical and demographic factors of NSCLC patients treated with immunotherapy. Smoking seems to be associated with an increased abundance of macrolides, lincosamides, streptogramins and vancomycin core resistome. The resistome of patients with progression disease appears to be more abundant and diverse, with significantly higher levels of genomic markers of resistance to lincosamides (lnuC). The resistance genes lnuC, msrD, ermG, aph(6), fosA were correlated with progression-free survival or/and overall survival, thus may be considered as factors potentially impacting the disease.ConclusionThe results indicate that the intestinal resistome of NSCLC patients with immune checkpoint inhibitors treatment differs depending on the response to immunotherapy, with several distinguished markers. Since it might impact treatment efficacy, it must be examined more deeply

Quasispecies Composition of Small Ruminant Lentiviruses Found in Blood Leukocytes and Milk Epithelial Cells

Small ruminant lentiviruses (SRLVs) exist as populations of closely related genetic variants, known as quasispecies, within an individual host. The privileged way of SRLVs transmission in goats is through the ingestion of colostrum and milk of infected does. Thus, characterization of SRLV variants transmitted through the milk, including milk epithelial cells (MEC), may provide useful information about the transmission and evolution of SRLVs. Therefore, the aim of this study was to detect SRLVs in peripheral blood leukocytes (PBLs) and milk epithelial cells of goats naturally infected with SRLVs and perform single nucleotide variations analysis to characterize the extent of genetic heterogeneity of detected SRLVs through comparison of their gag gene sequences. Blood and milk samples from 24 seropositive goats were tested in this study. The double immunolabeling against p28 and cytokeratin demonstrated that milk epithelial cells originated from naturally infected goats were infected by SRLVs. Moreover, PCR confirmed the presence of the integrated SRLVs proviral genome indicating that MECs may have a role as a reservoir of SRLVs and can transmit the virus through milk. The blood and MEC derived sequences from 7 goats were successfully sequenced using NGS and revealed that these sequences were genetically similar. The MEC and blood-derived sequences contained from 3 to 30 (mean, 10.8) and from 1 to 10 (mean, 5.4) unique SNVs, respectively. In five out of seven goats, SNVs occurred more frequent in MEC derived sequences. Non-synonymous SNVs were found in both, PBLs and MEC-derived sequences of analyzed goats and their total number differed between animals. The results of this study add to our understanding of SRLVs genomic variability. Our data provides evidence for the existence of SRLVs quasispecies and to our knowledge, this is the first study that showed quasispecies composition and minority variants of SRLVs present milk epithelial cells

Whole-Genome Sequencing-Based Characterization of Listeria monocytogenes from Fish and Fish Production Environments in Poland

Listeria monocytogenes, an important foodborne pathogen, may be present in different kinds of food and in food processing environments where it can persist for a long time. In this study, 28 L. monocytogenes isolates from fish and fish manufactures were characterized by whole genome sequencing (WGS). Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with publicly available genomes of L. monocytogenes strains recovered worldwide from food and from humans with listeriosis. All but one (96.4%) of the examined isolates belonged to molecular serogroup IIa, and one isolate (3.6%) was classified to serogroup IVb. The isolates of group IIa were mainly of MLST sequence types ST121 (13 strains) and ST8 (four strains) whereas the isolate of serogroup IVb was classified to ST1. Strains of serogroup IIa were further subtyped into eight different sublineages with the most numerous being SL121 (13; 48.1% strains) which belonged to six cgMLST types. The majority of strains, irrespective of the genotypic subtype, had the same antimicrobial resistance profile. The cluster analysis identified several molecular clones typical for L. monocytogenes isolated from similar sources in other countries; however, novel molecular cgMLST types not present in the Listeria database were also identified

Salmonella and Antimicrobial Resistance in Wild Rodents—True or False Threat?

Transmission of pathogenic and resistant bacteria from wildlife to the bacterial gene pool in nature affects the ecosystem. Hence, we studied intestine content of five wild rodent species: the yellow-necked wood mouse (Apodemus flavicollis, n = 121), striped field mouse (Apodemus agrarius, n = 75), common vole (Microtus arvalis, n = 37), bank vole (Myodes glareolus, n = 3), and house mouse (Mus musculus, n = 1) to assess their potential role as an antimicrobial resistance (AMR) and Salmonella vector. The methods adopted from official AMR monitoring of slaughtered animals were applied and supplemented with colistin resistance screening. Whole-genome sequencing of obtained bacteria elucidated their epidemiological relationships and zoonotic potential. The study revealed no indications of public health relevance of wild rodents from the sampled area in Salmonella spread and their limited role in AMR dissemination. Of 263 recovered E. coli, the vast majority was pan-susceptible, and as few as 5 E. coli showed any resistance. In four colistin-resistant strains neither the known mcr genes nor known mutations in pmr genes were found. One of these strains was tetracycline-resistant due to tet(B). High diversity of virulence factors (n = 43) noted in tested strains including ibeA, cdtB, air, eilA, astA, vat, pic reported in clinically relevant types of enteric E. coli indicate that rodents may be involved in the ecological cycle of these bacteria. Most of the strains represented unique sequence types and ST10805, ST10806, ST10810, ST10824 were revealed for the first time, showing genomic heterogeneity of the strains. The study broadened the knowledge on phylogenetic diversity and structure of the E. coli population in wild rodents

Draft Genome Sequences of Six Isolates of the Bacillus cereus Group Isolated from Pet Reptiles

International audienceBacteria of the Bacillus cereus group are Gram-positive rods and are widespread in nature, but little information is currently available about their presence in reptiles. Here, we report draft genome sequences of six Bacillus isolates belonging to three species, namely, Bacillus cereus, Bacillus paranthracis, and Bacillus toyonensis, isolated from pet reptiles in Poland

Mink SARS-CoV-2 infection in Poland – short communication

Since April 2020, when the first SARS-CoV-2 infection was reported in mink and subsequently in mink farm workers in the Netherlands, it has been confirmed that human-to-mink and mink-to-human transmission can occur. Later, SARS-CoV-2 infections in mink were reported in many European and North American countries

Poszukiwanie przyczyn oporności na immunoterapię pembrolizumabem u chorej na gruczołowego raka płuca z ekspresją PD-L1 — mikrobiom jelitowy „pod lupą”

Immunoterapia anty-PD-1 lub PD-L1 u niektórych chorych na niedrobnokomórkowego raka płuca (NDRP) może okazać się nieskuteczna, pomimo wysokiego odsetka komórek nowotworowych z ekspresją PD-L1 (≥ 50%). TMB (tumor mutation burden), status palenia tytoniu oraz niskie zróżnicowanie mikrobiomu jelitowego mogą wiązać się z brakiem skuteczności leczenia inhibitorami immunologicznych punktów kontroli u chorych na NDRP. Prezentowany w niniejszej pracy przypadek dotyczy niepalącej chorej na gruczołowego raka płuca, u której pomimo wysokiego odsetka komórek nowotworowych PD-L1 pozytywnych (50%) terapia pembrolizumabem okazała się nieskuteczna. U pacjentki wykonano sekwencjonowanie nowej generacji (NGS, next generation sequencing) z zastosowaniem panelu FOCUS pozwalającego na analizę 52 genów, których uszkodzenia są związane z różnymi typami guzów litych, w tym z rakiem płuca. Zaobserwowano zmiany genetyczne o statusie benign, co oznacza, że nie mają one w chwili obecnej znaczenia klinicznego dla chorych na NDRP. W międzyczasie wykonano profilowanie mikrobiomu jelitowego chorej, ze względu na to, że jego skład może być decydującym czynnikiem braku odpowiedzi na immunoterapię u chorych z wysoką ekspresją PD-L1 i bez mutacji kierujących (driver mutations). U opisywanej chorej zaobserwowano niskie zróżnicowanie bakterii występujących w jelitach z zauważalnym stanem dysbiozy (dysbakteriozy). Obecność bakterii Akkermansia, Enterococcaceae, Bifidobacteriaceae czy Coriobacteriaceae, zwłaszcza obecność Akkermansia mucinifila, wydaje się być czynnikiem korzystnym w odniesieniu do możliwości uzyskania odpowiedzi na immunoterapię oraz wydłużenia czasu wolnego od progresji (PFS, progression-free survival). W mikrobiomie jelitowym opisywanej chorej nie stwierdzono obecności bakterii z gromady Verrucomicrobia, do której należy A. mucinifila. Ponadto stwierdzono jedynie 0,011% bakterii z rodziny Enterococcaceae. Badania nad mikrobiomem jelitowym u chorych na nowotwory otrzymujących immunoterapię wydają się niezbędne w celu prawidłowego zrozumienia wpływu składu mikrobiomu na skuteczność tej metody leczenia

Poszukiwanie przyczyn oporności na immunoterapię pembrolizumabem u chorej na gruczołowego raka płuca z ekspresją PD-L1 – mikrobiom jelitowy „pod lupą”

Anti-PD-1 or PD-L1 immunotherapy in some patients with non-small cell lung cancer (NSCLC) may not be effective, despite the high percentage of cancer cells with PD-L1 expression (≥ 50%). TMB (tumor mutation burden), smoking status and low intestinal microbiome diversity may be associated with lack of efficacy of immune checkpoints inhibitors treatment in NSCLC patients. The case presented here concerns a non-smoking female patient with lung adenocarcinoma, in whom, despite the high percentage of PD-L1 positive tumor cells (50%), pembrolizumab therapy was ineffective. Next generation sequencing (NGS) was performed using the FOCUS panel allowing the analysis of 52 genes whose damage is associated with various types of solid tumors, including lung cancer. Benign genetic changes clinically irrelevant for patients with non-small cell lung cancer have been observed. In the meantime, profiling of the patient’s intestinal microbiome was performed, due to the fact that the composition of the intestinal microbiome may be a decisive factor in the lack of response to immunotherapy in patients with high PD-L1 expression and no driver mutations. Low diversity of bacteria in the intestines, with a noticeable dysbiosis (dysbacteriosis), was observed. The presence of bacteria Akkermansia, Enterococcaceae, Bifidobacteriaceae or Coriobacteriaceae, especially the presence of Akkermansia mucinifila seems to be a favourable factor of the possibility of obtaining response to immunotherapy and prolongation of progression-free survival (PFS). In the intestinal microbiome of the presented case, no bacteria from the Verrucomicrobia phylum, to which A. mucinifila belongs, were found. In addition, only 0.011% of Enterococcaceae were found. Studies on the intestinal microbiome in cancer patients receiving immunotherapy appear to be necessary to correctly understand the effect of microbiome composition on the effectiveness of this treatment method.