This study describes the first full genomic sequence of an mcr-9 and bla_VIM-4-carrying multidrug-resistant Enterobacter hormaechei clinical isolate from Egypt. The strain was isolated in April 2015 from the sputum of a patient in Cairo, Egypt. The mcr-9 and bla_VIM-4 genes were identified by PCR screening and DNA sequencing; the isolate was subjected to antimicrobial susceptibility testing, conjugation experiments, and whole genomic sequencing. mcr-9 and bla_VIM-4 were carried by an IncHI2 plasmid, pAMS-38a (281,121 bp in size); the plasmid also carried genes conferring resistance against sulfonamides (sul1), quinolones (qnrA1), trimethoprim (dfrA1), β-lactams (bla_TEM-1B), aminoglycosides (aac (6’)-II, aadA23, aadA2b, and ant(2’’)-Ia). The strain was susceptible to colistin (MIC, <0.25 μg/mL); this could be due to the absence of the qseC/qseB regulatory system located downstream of mcr-9 in Enterobacterales, which is involved in the induction of colistin-resistance. The genetic context of mcr-9 and bla_VIM-4 was identified as IS1-mcr-9-IS903-pcoS-∆pcoE-rcnA and intI1-bla_VIM-4—aac (6’)-II-dfrA1-∆aadA23-smr-ISPa21-qacE∆1, respectively. This is the first report of an mcr-9 and bla_VIM-4 /IncHI2-carrying multidrug-resistant E. hormaechei clinical isolate from Africa and the Middle East. Plasmids of the IncHI2 group and the two insertion sequences (IS1, and IS903) might be the main vehicles for dissemination of mcr-9. Further screening for mcr-9 is essential for identifying its incidence and to prevent its dissemination.

The plasmid-mediated tet (X7) conferring high-level tigecycline resistance was identified in five mcr-1.1 -positive Escherichia coli strains (ST10 [ n = 3] and ST155 [ n = 2]) isolated from chickens in Egypt. Two fosfomycin-resistant fosA4 -carrying IncFII plasmids (⁓79 kb in size) were detected.

Carbapenem and colistin antibiotics are often the last resort treatment for severe infections caused by multidrug-resistant bacteria (1-3).…

This study was conducted to characterize carbapenemase-producing Klebsiella pneumoniae and Acinetobacter baumannii isolated from fresh vegetables in Japan. Two K. pneumoniae (AO15, and AO22) and one A. baumannii (AO22) isolates collected from vegetables in the Higashihiroshima city, Japan and subjected to antimicrobial susceptibility testing, conjugation experiments and complete genome sequence using Illumina MiniSeq and Oxford Nanopore sequencing platforms. The two K. pneumoniae isolates were clonal, belonging to ST15 and were detected to carry 19 different antimicrobial resistance genes, including bla_NDM-1. Both the isolates carried bla_NDM-1 on a self-transmissible IncFII(K):IncR plasmid of 122,804 bp in size with other antimicrobial resistance genes against aminoglycosides (aac(69)-Ib, aadA1, aph(39)-VI), β-lactams (bla_CTXM-15, bla_OXA-9, bla_TEM-1A), fluoroquinolones (aac(69)-Ib-cr), and quinolones (qnrS1). A. baumannii AO22 carried bla_OXA-66 on the chromosome, while bla_OXA-72 was found as two copies on a GR2-type plasmid of 10,880 bp in size. Interestingly, A. baumannii AO22 harbored AbaR4-like genomic resistance island (GI) of 41,665 bp carrying antimicrobial resistance genes against tetracycline [tet(B)], sulfonamides (sul2), and streptomycin (strAB). Here, we identified Japanese carbapenemase-producing Gram-negative bacterias isolated from vegetables posing a food safety issue and a public health concern. Additionally, we reported a GR2-type plasmid carrying two copies of bla_OXA-72 and an AbaR4-like resistance island from a foodborne A. baumannii. IMPORTANCE Carbapenemase-producing Gram-negative bacteria (CPGNB) cause severe health care-associated infections and constitute a major public health threat. Here, we investigated the genetic features of CPGNB isolated from fresh vegetable samples in Japan and found CPGNB, including Klebsiella pneumoniae and Acinetobacter baumannii, with dissimilar carbapenemases. The rarely described NDM carbapenemase in Japan was detected in two K. pneumoniae isolates. A. baumannii isolate, identified in this study, carried bla_OXA-66 on the chromosome, while bla_OXA-72 was found as two copies on a GR2-type plasmid. This study illustrated that even one fresh ready-to-eat vegetable sample might serve as a significant source of resistance genes (bla_NDM-1, bla_OXA-72, bla_CTX-M-14b, and bla_CTX-M-15) to frontline and clinically important antibiotics (carbapenems and cephalosporins). Furthermore, the detection of these organisms in fresh vegetables in Japan is alarming and poses a food safety issue and a public health concern.

Background and Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) is a major concern in Jordanian hospitals in terms of infection control. The purpose of this study was to identify the resistance patterns of Staphylococcus aureus strains isolated from surfaces of critical locations within the Al-Karak Governmental Hospital in 2019. Additionally, the study aimed to conduct whole-genome sequencing on the isolates. Materials and Methods: In February 2019, fourteen S. aureus strains were isolated from surfaces in critical sites in the Al-Karak Governmental Hospital. These isolates underwent antibiogram testing to determine their resistance profile. Genome sequencing using the Illumina MiSeq platform was applied to the extracted DNA from these isolates. The genomic data, including coding sequences, were analyzed to identify lineage, resistance genes, and plasmids. Results: The antibiogram results revealed that 11 of the 14 isolates were resistant to oxacillin, 6 to linezolid, and 1 to rifampicin, while none showed resistance to chloramphenicol. Eleven isolates were identified as MRSA, with a novel spa type (t4407) not previously reported in Jordan. High-quality sequencing data were obtained for only one isolate, i.e., A29, the genome showed 2,789,641 bp with a 32.7% GC content and contained 2650 coding sequences. Genomic analysis indicated the ST6 lineage, mecA gene (SCCmec type IVa(2B)), and a hybrid plasmid (pJOR_blaZ) carrying the blaZ gene for β-lactam resistance. Genomic data were deposited in NCBI (CP104989). The A29 genome closely resembled an MRSA genome isolated from a Danish hospital in 2011. The SNP analysis revealed identical antimicrobial resistance genes in these two genomes. Conclusions: This study unveils the first genomic sequence of an MRSA isolate from Jordan, marked by distinctive genotypic traits. The findings enhance our understanding of the MRSA types circulating in Jordan and the region and substantiate the phenomenon of intercontinental MRSA transmission.

We developed two multiplex polymerase chain reactions (PCRs) for the detection of extended-spectrum β-lactamases (ESBLs), plasmid-mediated AmpC β-lactamases, aac(6′)-Ib gene, and integrase genes (intI1, intI2, and intI3) in class 1, 2, and 3 integrons in Gram-negative bacteria. We evaluated the PCRs using 109 Gram-negative isolates from non-organic (ANO) and organic (AO) vegetables and fruits. Screening of ANO substances identified five SHV, one TEM-1, one CTX-M, 20 AmpC-CS, and two intI1 positives. DNA sequencing revealed CTX-M in Pantoea spp. was bla_RANH-2, a plasmid-mediated CTX-M related ESBL gene only found in Rahnella spp. Of the 20 AmpC-CS positives, 10 were CMY/MIR/ACT/EC (3 new variants), eight were ACT, one was AZECL, and one was new Pseudomonas-related AmpC family. Screening of AO substances identified 11 SHV, two TEM-1, three CTX-M (one OXY-2, two CTX-M-14/-15), two OXA-9, 13 AmpC-CS and one intI1 positives. The 13 AmpC-CS positives were five CMY/MIR/ACT/EC, three ACT, one MOX-12 variant, and four ADC (one ADC-25 and three new variants). We developed a rapid, easy-to-perform, low-cost, and reliable multiplex PCR system for screening clinically relevant β-lactamases and integrons in Gram-negative bacteria. We showed the prevalence of ESBLs and AmpC β-lactamases among our panel of ampicillin-resistant Gram-negative strains and detection of NDM and OXA carbapenemases.