Antimicrobial resistance (AMR) in Helicobacter pylori is increasing and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to comprehensively analyze the H. pylori resistome and phylogeny in order to characterize Israeli H. pylori. Israeli H. pylori isolates (n = 48) underwent antimicrobial susceptibility testing (AST) against five antimicrobials and WGS analysis. Literature review identified 111 mutations reported to correlate with phenotypic resistance to these antimicrobials. Analysis was conducted via our in-house bioinformatics pipeline targeting point mutations in the relevant genes (pbp1A, 23S rRNA, gyrA, rdxA, frxA, and rpoB) in order to assess genotype-to-phenotype correlation. Resistance rates of study isolates were as follows: clarithromycin 54%, metronidazole 31%, amoxicillin 10%, rifampicin 4%, and levofloxacin 2%. Genotype-to-phenotype correlation was inconsistent; for every analyzed gene at least one phenotypically susceptible isolate was found to have a mutation previously associated with resistance. This was also observed regarding mutations commonly used in commercial kits to diagnose AMR in H. pylori cases. Furthermore, 11 novel point mutations associated with a resistant phenotype were detected. Analysis of a unique set of H. pylori isolates demonstrates that inferring resistance phenotypes from WGS in H. pylori remains challenging and should be optimized further.

In disenfranchised communities, untreated greywater (wastewater without sewage) is often environmentally discharged, resulting in potential human exposure to antimicrobial-resistant bacteria (ARB), including extended-spectrum beta-lactamase (ESBL) producers. We sought to examine the abundance of ARB, specifically ESBLs, and antimicrobial resistance genes (ARGs) in greywater from off-grid, pastoral Bedouin villages in Southern Israel. Greywater samples (n = 21) collected from five villages were analyzed to enumerate fecal coliforms and Escherichia coli. ESBL producers were recovered on CHROMagar ESBL and confirmed by VITEK^®2 (bioMerieux, Marcy l’Etoile, France) for identification and antimicrobial susceptibility testing. Total genomic DNA was extracted from greywater samples and quantitative PCR (qPCR) was used to determine relative abundance (gene copies/16S rRNA gene) of class 1 integron-integrase intI1, bla_TEM, bla_CTX-M-32, sul1, and qnrS. The mean count of presumptive ESBL-producing isolates was 4.5 × 10⁶ CFU/100 mL. Of 81 presumptive isolates, 15 ESBL producers were recovered. Phenotypically, 86.7% of ESBL producers were multi-drug resistant. Results from qPCR revealed a high abundance of intI1 (1.4 × 10⁻¹ gene copies/16S rRNA), sul1 (5.2 × 10⁻² gene copies/16S rRNA), and qnrS (1.7 × 10⁻² gene copies/16S rRNA) followed by bla_TEM (3.5 × 10⁻³ gene copies/16S rRNA) and bla_CTX-M-32 (2.2 × 10⁻⁵ gene copies/16S rRNA). Results from our study indicate that greywater can be a source of ARB, including ESBL producers, in settings characterized by low sanitary conditions and inadequate wastewater management.

Brucella melitensis is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of B. melitensis. Eighteen B. melitensis isolates from Southern Israel were sequenced using Illumina and the Oxford Nanopore (ONP) MinION, and hybrid assemblies were generated with ONP long reads scaffolded on Illumina short reads. Short reads were assembled with INNUca with SPADes, long reads and hybrid with dragonflye. Abricate with the virulence factor database (VFDB) and in silico PCR (for the genes BetB, BPE275, BSPB, manA, mviN, omp19, perA, PrpA, VceC, and ureI) were used for identifying virulence genes, and a total of 61 virulence genes were identified in short-read, long-read, and hybrid assemblies of all 18 isolates. The phylogenetic analysis using long-read assemblies revealed several inconsistencies in cluster assignment as compared to using hybrid and short-read assemblies. Overall, hybrid assembly provided the most comprehensive data, and stand-alone short-read sequencing provided comparable data to stand-alone long-read sequencing regarding virulence genes. For genomic epidemiology studies, stand-alone ONP sequencing may require further refinement in order to be useful in endemic settings.

Objective: Hurricanes Sandy and Irene damaged and destroyed homes, businesses, and infrastructure, and recovery after these storms took years. The goal of this article was to learn from the lived experience of local-level decision-makers actively involved in the long-term disaster recovery process after Hurricanes Irene and Sandy. Respondents provided professional recommendations, based on their experience, to assist other organizations in preparing for, responding to, and recovering from disasters.Methods: Semi-structured interviews were conducted with professionals actively involved in recovery from Hurricane Irene or Hurricane Sandy in 5 different communities. Transcripts were qualitatively analyzed.Results: Respondents’ advice fell into 5 main categories: planning and evaluation, education and training, fundraising and donations management, building relationships, and disaster behavioral health.Conclusions: The lived experience of those in disaster recovery can provide guidance for planning, education, and training both within and outside their communities in order to better respond to and recover from future disasters. These data help to facilitate a community of practice by compiling and sharing the lived experience of leaders who experienced large-scale disasters, and the outcomes of this analysis help to show what areas of planning require special attention in the phases of preparedness, response, and recovery. (Disaster Med Public Health Preparedness. 2016;10:623–630)

Extended-spectrum β-lactamases (ESBLs) are a growing public health threat, and one key human exposure point is through livestock and the food supply. Understanding microbiome factors associated with fecal ESBL carriage can help detect and ideally assist with controlling and preventing ESBL dissemination among livestock. The objective of this study was to investigate the diversity and composition of the heifer fecal microbiota in ESBL-producing Enterobacterales (ESBL-PE) carriers and noncarriers. A total of 59 fecal samples were collected from replacement heifers between 12 and 18 months old from eight dairy farms in central Israel. Genomic DNA was extracted, and 16S rRNA amplicon sequencing was performed (Illumina short reads), focusing on a comparison between 33 ESBL-PE carriers (55.9%) and 26 (44.1%) noncarriers. Samples were analyzed and compared using QIIME2 (DADA2 pipeline and taxonomic assignment with SILVA database) and associated R packages for alpha and beta diversity and taxonomic abundances. Alpha diversity (Shannon diversity) and beta diversity (unweighted UniFrac) showed no significant difference between ESBL-PE carriers and noncarriers. Heifers from farms feeding calves with pooled colostrum had higher ESBL-PE carriage rates than heifers from farms feeding with individual mother colostrum (p < 0.001). Taxonomical abundance analysis revealed that the most common bacterial phyla were Bacteroidetes (44%) and Firmicutes (38%). There was no significant difference in taxonomic composition between ESBL-PE carriers and noncarriers at the phylum and genus levels. However, LEfSe biomarker discovery analysis identified several genera which were significantly different between carriers and noncarriers. For example, Prevotellacaea, Bacteroides, Rikenellaceae, and uncultured Bacteroidales were more abundant in ESBL carriers than noncarriers. Some aspects of microbiota composition differ between ESBL carriers and noncarriers in dairy heifers, specifically the abundance of certain genera. Feeding with pooled colostrum may play a role in that assembly. These could potentially serve as markers of ESBL-PE carriage. However, further research is needed to determine whether these observed differences have a significant impact on colonization with ESBL-PE.