scholarly journals Emergence of ST63 Pandrug-Resistant Acinetobacter pittii Isolated From an AECOPD Patient in China

Author(s):  
Ling Yang ◽  
Ning Dong ◽  
Chen Xu ◽  
Lianwei Ye ◽  
Sheng Chen

Acinetobacter sp. is among the ESKAPE organisms which represent the major nosocomial pathogens that exhibited a high resistance rate. A. pittii, frequently associated with antimicrobial resistance particularly to carbapenems, is one of the most common Acinetobacter species causing invasive infection. Pandrug resistant A. pittii has rarely been reported. Here, we report the case of a patient with acute exacerbations of chronic obstructive pulmonary disease three years after double lung transplantation and developed severe pneumonia associated with pandrug resistant A. pittii infection. Phenotypic and genomic characteristics of this pandrug resistant isolate (17-84) was identified, and the mechanisms underlying its resistance phenotypes were analyzed. Isolate 17-84 belonged to ST63, carried a non-typable and non-transferable plasmid encoding multiple acquired resistance genes including carbapenemase gene blaOXA-58. Point mutations and acquired resistance genes were identified which were associated with different drug resistance phenotypes. To our knowledge, this is the first detailed phenotypic and genomic characterization of PDR A. pittii causing severe infections in clinical settings. Findings from us and others indicate that A. pittii could serve as a reservoir for carbapenem determinants. The emergence of such a superbug could pose a serious threat to public health. Further surveillance of PDR A. pittii strains and implementation of stricter control measures are needed to prevent this emerging pathogen from further disseminating in hospital settings and the community.

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Gamal Wareth ◽  
Christian Brandt ◽  
Lisa D. Sprague ◽  
Heinrich Neubauer ◽  
Mathias W. Pletz

Abstract Background Acinetobacter baumannii ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole-genome sequencing (WGS) was applied to identify the acquired or mutational variants of antimicrobial resistance (AMR) genes in 85 German A. baumannii strains utilizing Illumina technology. Additionally, the whole genome of 104 German isolates deposited in the NCBI database was investigated. Results In-silico analysis of WGS data revealed wide varieties of acquired AMR genes mediating resistance mostly to aminoglycosides, cephalosporins, carbapenems, sulfonamides, tetracyclines and macrolides. In the 189 analyzed genomes, the ant (3″)-IIa conferring resistance to aminoglycosides was the most frequent (55%), followed by blaADC.25 (38.6%) conferring resistance to cephalosporin, blaOXA-23 (29%) and the blaOXA-66 variant of the intrinsic blaOXA-51-likes (26.5%) conferring resistance to carbapenems, the sul2 (26%) conferring resistance to sulfonamides, the tet. B (19.5%) conferring resistance to tetracycline, and mph. E and msr. E (19%) conferring resistance to macrolides. blaTEM variants conferring resistance to cephalosporins were found in 12% of genomes. Thirteen variants of the intrinsic blaOXA-51 carbapenemase gene, blaOXA-510 and blaADC-25 genes were found in isolates obtained from dried milk samples. Conclusion The presence of strains harboring acquired AMR genes in dried milk raises safety concerns and highlights the need for changes in producing dried milk. Acquired resistance genes and chromosomal gene mutation are successful routes for disseminating AMR determinants among A. baumannii. Identification of chromosomal and plasmid-encoded AMR in the genome of A. baumannii may help understand the mechanism behind the genetic mobilization and spread of AMR genes.


2021 ◽  
Author(s):  
Carla Rodrigues ◽  
Siddhi Desai ◽  
Virginie Passet ◽  
Devarshi Gajjar ◽  
Sylvain Brisse

Background: The rapid emergence of multidrug-resistant Klebsiella pneumoniae (Kp) is largely driven by the spread of specific clonal groups (CG). Of these, CG147 includes 7-gene MLST sequence types ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147. Methods: Antimicrobial susceptibility testing (EUCAST guidelines) and genome sequencing (Illumina and Oxford Nanopore technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes (NCBI, May 2019). CG147 evolution was inferred within a temporal phylogenetic framework (BEAST) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, PHASTER, ICEFinder and CRISPRCasFinder). Results: Strain DJ had a pandrug resistance phenotype. Its genome comprised 7 plasmids and 1 linear phage-plasmid. Four carbapenemase genes were detected: blaNDM-5 and 2 copies of blaOXA-181 in the chromosome, and a second copy of blaNDM-5 on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63% carried a carbapenemase gene and 83% harbored blaCTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype IV-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74%, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20%, 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Further, subclades within ST147-KL64 differed in the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system. Conclusions: K. pneumoniae clonal group CG147 comprises pandrug- or extensively-resistant isolates and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomal blaNDM-5. Its emergence is driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo-spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.


Author(s):  
Pierre Danneels ◽  
Maria Concetta Postorino ◽  
Alessio Strazzulla ◽  
Nabil Belfeki ◽  
Aurelia Pitch ◽  
...  

Introduction. Treatment of Haemophilus influenzae (Hi) pneumonia is on concern because resistance to amoxicillin is largely diffused. This study describes the evolution of resistance to amoxicillin and amoxicillin/clavulanic acid (AMC) in Hi isolates and characteristics of patients with Hi severe pneumonia. Methods. A monocentric retrospective observational study including patients from 2008 to 2017 with severe pneumonia hospitalized in ICU. Evolution of amoxicillin and AMC susceptibility was showed. Characteristics of patients with Hi pneumonia were compared to characteristics of patients with Streptococcus pneumoniae (Sp) pneumonia, as reference. Risk factors for amoxicillin resistance in Hi were investigated. Results. Overall, 113 patients with Hi and 132 with Sp pneumonia were included. The percentages of AMC resistance among Hi strains decreased over the years (from 10% in 2008-2009 to 0% in 2016-2017) while resistance to amoxicillin remained stable at 20%. Also, percentages of Sp resistant strains for amoxicillin decreased over years (from 25% to 3%). Patients with Hi pneumonia experienced higher prevalence of bronchitis (18% vs. 8%, p=0.02, chronic obstructive pulmonary disease (43% vs. 30% p=0.03), HAP (18% vs. 7%, p=0.01, ventilator-associated pneumonia (27% vs. 17%, p=0.04, and longer duration of mechanical ventilation (8 days vs. 6 days, p=0.04) than patients with Sp pneumonia. Patients with Sp pneumonia had more frequently local complications than patients with Hi pneumonia (17% vs. 7%, p=0.03). De-escalation of antibiotics was more frequent in patients with Sp than in patients with Hi (67% vs. 53%, p=0.03). No risk factors were associated with amoxicillin resistance among patients with Hi pneumonia. Conclusions. Amoxicillin resistance was stable over time, but no risk factors were detected. AMC resistance was extremely low, suggesting that AMC could be used for empiric treatment of Hi pneumonia, as well as other molecules, namely, cephalosporins. Patients with Hi pneumonia had more pulmonary comorbidities and severe diseases than patients with Sp pneumonia.


Author(s):  
Maria Luisa Ricci ◽  
Maria Cristina Rota ◽  
Maria Grazia Caporali ◽  
Antonietta Girolamo ◽  
Maria Scaturro

Legionnaires’ disease (LD) is a severe pneumonia caused by bacteria belonging to the genus Legionella. This is a major public health concern and infections are steadily increasing worldwide. Several sources of infection have been identified, but they have not always been linked to human isolates by molecular match. The well-known Legionella contamination of private homes has rarely been associated with the acquisition of the disease, although some patients never left their homes during the incubation period. This study demonstrated by genomic matching between clinical and environmental Legionella isolates that the source of an LD cluster was a private building. Monoclonal antibodies and sequence-based typing were used to type the isolates, and the results clearly demonstrated the molecular relationship between the strains highlighting the risk of contracting LD at home. To contain this risk, the new European directive on the quality of water intended for human consumption has introduced for the first time Legionella as a microbiological parameter to be investigated in domestic water systems. This should lead to a greater attention to prevention and control measures for domestic Legionella contamination and, consequently, to a possible reduction in community acquired LD cases.


AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Quan Li ◽  
Jian Yin ◽  
Zheng Li ◽  
Zewei Li ◽  
Yuanzhao Du ◽  
...  

AbstractSalmonella is an important food-borne pathogen associated with public health and high economic losses. To investigate the prevalence and the characteristics of Salmonella in a pig slaughterhouse in Yangzhou, a total of 80 Salmonella isolates were isolated from 459 (17.43%) samples in 2016–2017. S. Derby (35/80, 43.75%) was the most prevalent, followed by S. Rissen (16/80, 20.00%) and S. Newlands (11/80, 13.75%). The highest rates of susceptibility were observed to cefoxitin (80/80, 100.0%) and amikacin (80/80, 100.0%), followed by aztreonam (79/80, 98.75%) and nitrofurantoin (79/80, 98.75%). The highest resistance rate was detected for tetracycline (65/80, 81.25%), followed by ampicillin (60/80, 75.00%), bactrim (55/80, 68.75%), and sulfisoxazole (54/80, 67.50%). Overall, 91.25% (73/80) of the isolates were resistant to at least one antibiotic, while 71.25% (57/80) of the isolate strains were multidrug resistant in the antimicrobial susceptibility tested. In addition, 86.36% (19/22) of the 22 antimicrobial resistance genes in the isolates were identified. Our data indicated that the resistance to certain antimicrobials was significantly associated, in part, with antimicrobial resistance genes. Furthermore, 81.25% (65/80) isolates harbored the virulence gene of mogA, of which 2 Salmonella Typhimurium isolates carried the mogA, spvB and spvC virulence genes at the same time. The results showed that swine products in the slaughterhouse were contaminated with multidrug resistant Salmonella commonly, especially some isolates carry the spv virulence genes. The virulence genes might facilitate the dissemination of the resistance genes to consumers along the production chain, suggesting the importance of controlling Salmonella during slaughter for public health.


2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S468-S468
Author(s):  
Mariawy Riollano ◽  
Deena Altman ◽  
shanna kowalsky ◽  
Stephanie Pan

Abstract Background Staphylococcus aureus is a well-known cause of hospital acquired infections. Methicillin resistant staphylococcus aureus (MRSA) colonization is a recognized risk factor for invasive infections. The neonatal population in the intensive care unit (NICU) is particularly vulnerable to these types of infections, resulting in high mortality and morbidity. However, only scant data is available to establish the risk for invasive disease in patients with Methicillin sensitive staphylococcus aureus (MSSA). As a result, surveillance and prevention strategies are only address for MRSA colonization. Here, we describe the clinical characteristics of S. aureus colonized patients identified in late 2018 during transmission events in a single center NICU. As a result of the targeted surveillance investigation for MRSA infection control measures, S. aureus colonization was stratified, and we were able to compare the differences in invasive disease between MRSA and MSSA. Methods This is a retrospective chart review of the 47 colonized patients identified during October 2018- January 2019 SA transmission events in single center NICU. Risk factors, clinical characteristics, and the hospital course of these cases, including the proportion of invasive illness were reviewed. Results We found that most clinical characteristic, risk factors, and hospital course were the same between MRSA and MSSA colonized infants (p values > 0.05). Additionally, there was no difference in the proportion of invasive infection between MRSA and MSSA colonized patients (p value > 0.05). The type of invasive infections identified were SSTI, bacteremia, and osteomyelitis. Conclusion The proportion of invasive infection was the same in MSSA and MRSA colonized patients. This data provides us with supportive material for future recommendations of infection control measures for MSSA colonized patients. Disclosures All Authors: No reported disclosures


BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuan Wu ◽  
Lin Yang ◽  
Wen-Ge Li ◽  
Wen Zhu Zhang ◽  
Zheng Jie Liu ◽  
...  

Abstract Background Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11 C. difficile isolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates. Results Isolates 10,010 and 12,038 carried a distinct deletion in tcdA compared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations in tcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes. Conclusions We concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.


Author(s):  
Е.Е. Краснова ◽  
В.В. Чемоданов ◽  
Е.Г. Кузнецова

Пневмония – острое инфекционно-воспалительное заболевание легких преимущественно бактериальной этиологии, характеризующееся выраженной в разной степени дыхательной недостаточностью, токсическими и респираторными нарушениями, локальными физикальными симптомами, а также инфильтративными изменениями на рентгенограмме. Заболеваемость внебольничными пневмониями повышается в октябре-декабре, достигая максимума в январе-апреле, коррелируя с сезонным повышением уровня острых респираторных вирусных инфекций. Схожесть симптомов дебюта пневмонии с проявлениями острых респираторных вирусных инфекций может привести к несвоевременной ее диагностике и, как следствие, к отсроченному началу лечения. Поэтому в период сезонной заболеваемости респираторными инфекциями должна повышаться настороженность врачей-педиатров в отношении внебольничной пневмонии. Антибактериальная терапия оказывает решающее влияние на прогноз пневмонии, поэтому при достоверном диагнозе или у больного в тяжелом состоянии с вероятным диагнозом ее следует начать незамедлительно. Выбор антибиотика в каждом случае внебольничной пневмонии проводят индивидуально с учетом природной активности препаратов в отношении предполагаемого возбудителя и их возможной приобретенной резистентности, тяжести и течения заболевания, наличия у пациента противопоказаний к использованию тех или иных антибиотиков. В статье приводятся сведения о диагностических критериях внебольничных пневмоний. Рассмотрены вопросы антибактериального лечения типичной нетяжелой пневмонии у детей разных возрастных групп амоксициллином с клавулановой кислотой и показана его эффективность. Результаты проведенного исследования позволяют заключить, что пероральное использование одного курса защищенного аминопенициллина эффективно при лечении типичной внебольничной нетяжелой пневмонии у детей разного возраста, о чем свидетельствует ликвидация основных клинических проявлений болезни в короткие сроки. Pneumonia is an acute infectious and inflammatory lung disease of predominantly bacterial etiology, characterized by respiratory failure, toxic and respiratory disorders, local physical symptoms, and infiltrative changes on the roentgenogram. The incidence of community-acquired pneumonia increases in October-December, reaching a maximum in January-April, correlating with the seasonal increase in the level of acute respiratory viral infections. The similarity of the symptoms of the onset of pneumonia with the manifestations of acute respiratory viral infections can lead to its untimely diagnosis and, as a consequence, to a delayed start of treatment. Therefore, during the period of seasonal morbidity with respiratory infections, the alertness of pediatricians in relation to community-acquired pneumonia should increase. Antibiotic therapy has a decisive influence on the prognosis of pneumonia, therefore, with a reliable diagnosis or in a patient in serious condition with a probable diagnosis, it should be started immediately. The choice of antibiotic in each case of community-acquired pneumonia is carried out individually, taking into account the natural activity of the drugs in relation to the alleged pathogen and their possible acquired resistance, the severity and course of the disease, the patient's contraindications to the use of certain antibiotics. The article provides information on the diagnostic criteria for community-acquired pneumonia. The issues of antibacterial treatment of typical non-severe pneumonia in children of different age groups with amoxicillin with clavulanic acid are considered and its effectiveness is shown. The results of the study allow us to conclude that the oral use of one course of protected aminopenicillin is effective in the treatment of typical community-acquired non-severe pneumonia in children of different ages, as evidenced by the elimination of the main clinical manifestations of the disease in a short time.


Acta Tropica ◽  
2009 ◽  
Vol 110 (1) ◽  
pp. 75-79 ◽  
Author(s):  
Shilpi Garg ◽  
Vishal Saxena ◽  
Swarna Kanchan ◽  
Pooja Sharma ◽  
Siddharth Mahajan ◽  
...  

2021 ◽  
Vol 04 (01) ◽  
pp. 57-81
Author(s):  
SHEENA WONG ◽  
GOH JING EN ◽  
DAVID KOH

A severe pneumonia of an unknown origin was reported in Wuhan, China in December 2019. The disease, now known as coronavirus disease 2019 (COVID-19), has evolved into a public health emergency of international concern and wreaked worldwide havoc. An unprecedented and vigorous scientific response has allowed the accelerated discovery of the virus and reliable diagnostic methods; a rapid characterization of the disease and its impacts so as to better apply precautionary and public health measures; and resulted in remarkable progress in the development of mitigation strategies, including the development of vaccines at breakneck speed. This paper provides a health perspective of the virus and the pandemic it caused, based on available best evidence. Controversies surrounding the origin of the virus, its incubation period and infectivity, presentation and course of the disease, testing, as well as treatments and vaccinations are highlighted. The pandemic response, including infection control measures, and considerations on mental and economic health, alongside physical health is discussed. Moving forward, it is important that the global community is aware and better informed. More resources are needed to strengthen public health systems and healthcare infrastructure and delivery. This virus has the potential to persist and become endemic and seasonal in communities. Thus, non-pharmaceutical interventions (e.g. wearing masks, frequent hand washing, etc.) might become the new normal in a post-pandemic world. The silver lining in the COVID-19 cloud may be the lessons it provides, so that we may be better prepared to respond to an inevitable next pandemic.


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