Nosocomial outbreak due to a novel sequence type of carbapenem-resistant Acinetobacter seifertii

BACKGROUND

Acinetobacter seifertii, a member of A baumannii-calcoaceticus complex, can be considered a pathogen of concern due to the presence of resistance genes. The aim of the study was to describe an outbreak of carbapenem-resistant A seifertii among neonates admitted to the neonatal intensive care unit (NICU) at a tertiary care hospital.

METHODS

All patients with carbapenem-resistant A seifertii diagnosed and admitted to the NICU from June 2023 to October 2023 were included. The presence of carbapenemase genes (blaIMP, blaVIM, blaNDM, blaKPC, blaGES, blaOXA-48-like, and blaOXA-23) was investigated by qPCR. Whole-genome sequencing (WGS) was performed by MiSeq (Illumina) and MinION (Nanopore) platforms. Fourier-transform infrared spectroscopy (IR Biotyper) was applied for microbial strain typing.

RESULTS

Eleven patients were affected and a set of measures were implemented at NICU to reduce the risk of transmission. The isolates exhibited identical resistance patterns; additionally, all isolates presented the blaNDM-1 gene and were grouped in the same cluster by IR Biotyper. The WGS revealed that the isolates belonged to a novel ST assigned as ST2712, and the blaNDM-1 was carried by the same plasmid type.

DISCUSSION

Our study has identified a novel strain of A seifertii carrying blaNDM-1 responsible for the outbreak, indicating its emergence in the institution.

CONCLUSIONS

This is the first report of carbapenem-resistant A seifertii ST2712. The use of WGS for genomic surveillance allowed understanding the dissemination of Carbapenem-resistant A baumannii, which is crucial in outbreak scenarios.

Drug resistance of Acinetobacter ssp. in patients with pneumonia in a Brazilian Pre-Amazon region during the pre-pandemic and pandemic periods of COVID-19

Antimicrobial resistance is a global public health threat that has been impacted by the COVID-19 pandemic. The aim of this study was to evaluate the resistance of Acinetobacter spp. isolated from patients with pneumonia in a Brazilian Pre-Amazon region during the pre-pandemic and pandemic periods of COVID-19. Bacterial strains were obtained from tracheal aspiration, sputum and bronchoalveolar lavage for diagnosis and phenotypic characterization. MALD-TOF was used to identify strains. The automated Phoenix and VITEK® 2 Compact system and the disc diffusion method were performed to determine the antimicrobial susceptibility profile. Were analyzed a total of 41,590 samples from patients admitted to hospitals of a Brazilian Pre-Amazon region, from January 2019 to December 2021. Of these, 162 isolates of Acinetobacter spp. were from the pre-pandemic period and 308 from the pandemic COVID-19. A. baumannii was the most prevalent species. Among the samples, 52% were male patients, aged over 60 years, hospitalized in intensive care units. Acinetobacter spp. showed higher rates of resistance to cefepime (79.1%), levofloxacin (77.8%), and ceftazidime (77%) in the pre-pandemic period and during the pandemic to piperacillin (72.4%), imipenem (71.6%) and ciprofloxacin (71.8%). Taken together, the data showed that A. baumannii was the most prevalent species among Acinetobacter spp., being more frequent among elderly patients admitted to the ICU. The strains presented high resistance to most antibiotics tested, mainly carbapenems. In addition, there was an increase in resistance to polymyxin B, which raises an alert since this is a therapeutic choice to treat infections caused by Acinetobacter spp. multidrug resistant.

Whole-plasmid analysis of NDM-1-producing Acinetobacter seifertii isolate and its fitness in several Acinetobacter species

OBJECTIVES

The aim of this study was to characterize an NDM-1-producing Acinetobacter seifertii isolates from a patient in South Korea.

METHODS

Antibiotic susceptibility testing and genotyping using multigene sequencing were performed and whole plasmid sequences were determined.

RESULTS

The genotype of A. seifertii was ST1899 and was resistant to ceftazidime, trimethoprim-sulfamethoxazole, and piperacillin-tazobactam, in addition to carbapenem. blaNDM-1 was surrounded by the ISAba125 insertion sequence within the structure of Tn125 in the 47 kb-sized plasmid. The plasmid exhibited a structure similar to that of other plasmids of diverse Acinetobacter sp. found worldwide. Transconjugation and the growth curve indicated that the plasmid was adapted to A. seifertii rather than other closely related Acinetobacter sp.

CONCLUSIONS

Acquisition of carbapenem resistance by horizontal transfer of the blaNDM-1-carrying plasmid from another Acinetobacter species was found with no growth defect.

Genome sequence of a tigecycline-resistant Acinetobacter seifertii recovered in human bloodstream infection in China

OBJECTIVES

The phylogenetic characteristics of Acinetobacter seifertii clinical strain are not well-studied. Here, we reported one tigecycline-resistant ST1612Pasteur A. seifertii isolated from bloodstream infections (BSI) in China.

METHODS

Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing (WGS) was performed and annotation was conducted using rapid annotations subsystems technology (RAST) server. Multilocus sequence typing (MLST), capsular polysaccharide (KL), and lipoolygosaccharide (OCL) were analysed using PubMLST and Kaptive. Resistance genes, virulence factors, and comparative genomics analysis were performed. Cloning, mutations of efflux pump-related genes, and expression level were further investigated.

RESULTS

The draft genome sequence of A. seifertii ASTCM strain is made up of 109 contigs with a total length of 4,074,640 bp. Based on the RAST results, 3923 genes that belonged to 310 subsystems were annotated. Acinetobacter seifertii ASTCM was ST1612Pasteur with KL26 and OCL4, respectively. It was resistant to gentamicin and tigecycline. ASTCM harboured tet(39), sul2, and msr(E)-mph(E), and one amino acid mutation in Tet(39) (T175A) was further identified. Nevertheless, the signal mutation failed to contribute to susceptibility change of tigecycline. Of note, several amino acid substitutions were identified in AdeRS, AdeN, AdeL, and Trm, which could lead to overexpression of adeB, adeG, and adeJ efflux pump genes and further possibly lead to tigecycline resistance. Phylogenetic analysis showed that a huge diversity was observed among A. seifertii strains based on 27-52,193 SNPs difference.

CONCLUSION

In summary, we reported a tigecycline-resistant ST1612Pasteur A. seifertii in China. Early detection is recommended to prevent their further spread in clinical settings.

The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany

Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.

Clinical and molecular characterization of Acinetobacter seifertii in Taiwan

OBJECTIVES

Acinetobacter seifertii, a new member of the Acinetobacter baumannii group, has emerged as a cause of severe infections in humans. We investigated the clinical and molecular characteristics of A. seifertii.

PATIENTS AND METHODS

This retrospective study enrolled 80 adults with A. seifertii bloodstream infection (BSI) at four medical centres over an 8 year period. Species identification was confirmed by MALDI-TOF MS, rpoB sequencing and WGS. Molecular typing was performed by MLST. Clinical information, antimicrobial susceptibility and the mechanisms of carbapenem and colistin resistance were analysed. Transmissibility of the carbapenem-resistance determinants was examined by conjugation experiments.

RESULTS

The main source of A. seifertii BSI was the respiratory tract (46.3%). The 28 day and in-hospital mortality rates of A. seifertii BSI were 18.8% and 30.0%, respectively. High APACHE II scores and immunosuppressant therapy were independent risk factors for 28 day mortality. The most common MLST type was ST553 (58.8%). Most A. seifertii isolates were susceptible to levofloxacin (86.2%), and only 37.5% were susceptible to colistin. Carbapenem resistance was observed in 16.3% of isolates, mostly caused by the plasmid-borne ISAba1-blaOXA-51-like genetic structure. A. seifertii could transfer various carbapenem-resistance determinants to A. baumannii, Acinetobacter nosocomialis and other A. seifertii isolates. Variations of pmrCAB and lpxCAD genes were not associated with colistin resistance of A. seifertii.

CONCLUSIONS

Levofloxacin and carbapenems, but not colistin, have the potential to be the drug of choice for A. seifertii infections. A. seifertii can transfer carbapenem-resistance determinants to other species of the A. baumannii group and warrants close monitoring.

Characterization of an Environmental Multidrug-Resistant Acinetobacter seifertii and Comparative Genomic Analysis Reveals Co-occurrence of Antimicrobial Resistance and Metal Tolerance Determinants

Acinetobacter calcoaceticus-Acinetobacter baumannii complex is considered one of the main causes of hospital-acquired infections. Acinetobacter seifertii was recently characterized within this complex and it has been described as an emergent pathogen associated with bacteremia. The emergence of multidrug-resistant (MDR) bacteria, including Acinetobacter sp., is considered a global public health threat and an environmental problem because MDR bacteria have been spreading from several sources. Therefore, this study aimed to characterize an environmental MDR A. seifertii isolate (SAb133) using whole genome sequencing and a comparative genomic analysis was performed with A. seifertii strains recovered from various sources. The SAb133 isolate was obtained from soil of a corn crop field and presented high MICs for antimicrobials and metals. The comparative genomic analyses revealed ANI values higher than 95% of relatedness with other A. seifertii strains than A. calcoaceticus-A. baumannii complex. Resistome and virulome analyses were also performed and showed different antimicrobial resistance determinants and metal tolerance genes as well as virulence genes related to A. baumannii known virulence genes. In addition, genomic islands, IS elements, plasmids and prophage-related sequences were detected. Comparative genomic analysis showed that MDR A. seifertii SAb133 had a high amount of determinants related to antimicrobial resistance and tolerance to metals, besides the presence of virulence genes. To the best of our knowledge, this is the first report of a whole genome sequence of a MDR A. seifertii isolated from soil. Therefore, this study contributed to a better understanding of the genetic relationship among the few known A. seifertii strains worldwide distributed.

An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017

Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.