Genomic Analysis of two NDM-1 Providencia stuartii Strains Recovered from a Single Patient

Abstract

In the last years, an increasing number of untreatable infections caused by drug-resistant microbes have impacted the health care system. Worldwide, infections caused by carbapenem-resistant (CR) Gram-negative bacilli have dramatically increased. Among the CR-Gram-negative bacilli, those producing carbapenemases, such as NDM-1, are the main concern. Different Enterobacterales harboring NDM-1 have been reported lately. Providencia stuartii, a member of the Morganellaceae family, is ubiquitous in the environment, but is also known to cause nosocomial infections. Here we describe the genomic analysis of two NDM-1-producing P. stuartii strains recovered from the same patient as well as other carbapenem resistant strains recovered from the same hospital. As a result of the genomic analysis thirteen resistance genes, including three to β-lactams (bla OXA-1 , bla TEM-1 , bla NDM-1 ), four to aminoglycosides (aphA6, aac(3)-IId, aac(2′)-Ia, aac(6′)-Ib-cr5), one to sulfonamides (sul1), two to chloramphenicol (catB3, catA3), one to rifampicin, one to bleomycin (ble), and one to tetracycline (tet(B)) were found. Moreover, a variety of mobile genetic elements, such as insertion sequences, plasmids and phage-related sequences, were found within P. stuartii genomes. The spread of carbapenem-resistant isolates remains a significant clinical and public health concern. Therefore, we considered that the detection of CR isolates is an essential step in addressing this problem.

Escalating antimicrobial resistance among Enterobacteriaceae: focus on carbapenemases

“…KPC-2, the most common CPase in the USA, emerged in North Carolina in 1996 52 , and spread within the USA 53,54 , South America 55 , Europe 30,56 , Israel 57 , South Africa 58 , Asia 1,[59][60][61] , and worldwide 30 . CRE is predominantly due to KPC-2 on plasmids or other MGEs (e.g., insertion sequences, and phage-related sequences) 62,63 . In Brazil, KPC-2 is the most common CPase, carried on plasmids among K. pneumoniae belonging to different international lineages (e.g., sequence type (ST)258, ST101, and ST15) 64 .…”

Dissemination of extensively drug-resistant NDM-producing Providencia stuartii in Europe linked to patients transferred from Ukraine, March 2022 to March 2023

“…P. stuartii is characterised by intrinsic resistance to aminopenicillins, early generation cephalosporins, colistin and tigecycline as well as its ability to acquire antimicrobial resistance (AMR) genes [4][5][6][7], including those associated with resistance to last-resort antibiotics, such as carbapenems. In addition, P. stuartii has been shown to cause hospital outbreaks and infections worldwide [5][6][7][9][10][11][12], further highlighting its public health relevance.…”

Providencia Species – Involvement in Pathology and Multidrug Resistance in a Romanian County Hospital

“…OXA-72 carbapemenase was detected in P. rettgeri. [1], [15], [16], [17] Resistance to these antibiotics may also be due to non-carbapenemase mechanisms consisting of changes in penicillin-binding proteins or in outer membrane proteins or activation of effluxpumps [1], [13], [18].…”