- Volume 70, Issue 11, 2021
Volume 70, Issue 11, 2021
- Reviews
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The enigma of Pacini’s Vibrio cholerae discovery
More LessDuring the 1854 cholera outbreak in Florence, Italy, Filippo Pacini documented that the cause of the infection was a bacterium. This conclusion was also independently reached by John Snow during the 1854 cholera outbreak in London. By using an epidemiological method, Snow found that the infection spread through a polluted water network. Snow identified a water pump as the source of the disease. After removing the infected handle of this pump, the cases of cholera rapidly began to decrease. A microscopic examination of the water showed organic impurities but no bacteria. This discovery was ignored during Snow’s lifetime. In contrast, through microscopy during the autopsies of cholera victims, Pacini observed that the disruption of their intestinal mucosa was closely associated with millions of the bacteria that he called Vibrio cholerae . Via histological techniques, Pacini detected that intestinal mucosa reabsorption dysfunction was the cause of debilitating diarrhoea, vomiting, severe dehydration and death. Nevertheless, his discovery of Vibrio cholerae was ignored during Pacini’s lifetime. A survey of Pacini’s autographic manuscripts suggests that Pacini and Snow may have shared mutual knowledge within their respective seminal papers. This survey also facilitates, for the first time, the creation of maps that illustrate the worldwide distribution of Pacini’s cholera papers from 1854 to 1881. The consistent neglect of Pacini’s discovery remains a true enigma.
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- JMM Profiles
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JMM Profile: Streptococcus pneumoniae: sugar-coated captain of the men of death
More LessStreptococcus pneumoniae is a highly adept human pathogen. A frequent asymptomatic member of the respiratory microbiota, the pneumococcus has a remarkable capacity to cause mucosal (pneumonia and otitis media) and invasive diseases (bacteremia, meningitis). In addition, the organism utilizes a vast battery of virulence factors for tissue and immune evasion. Though recognized as a significant cause of pneumonia for over a century, efforts to develop more effective vaccines remain ongoing. The pathogen’s inherent capacity to exchange genetic material is critical to the pneumococcus’ success. This feature historically facilitated essential discoveries in genetics and is vital for disseminating antibiotic resistance and vaccine evasion.
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- Antimicrobial Resistance
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Phenotypic and molecular evaluation of biofilm formation in Klebsiella pneumoniae carbapenemase (KPC) isolates obtained from a hospital of Pelotas, RS, Brazil
Introduction. A significant cause of mortality in the intensive care unit (ICU) is multidrug-resistant (MDR) Gram-negative bacteria, such as Klebsiella pneumoniae carbapenemase (KPC). Biofilm production is a key factor in KPC colonization and persistence in the host, making the treatment difficult.
Gap Statement. The aim of this study was to evaluate the antibiotic resistance, molecular and phenotypic biofilm profiles of 12 KPC isolates associated with nosocomial infection in a hospital in Pelotas, Rio Grande do Sul, Brazil.
Methodology. Clinical isolates were obtained from different sources, identified and characterized by antibiotic resistance and carbapenemase synthesis following the Clinical and Laboratory Standards Institute (CLSI) guidelines. Polymerase chain reaction (PCR) was used to evaluate the presence of carbapenemase (blaKPC ) and biofilm formation-associated genes (fimA, fimH, rmpA, ecpA, mrkD and wabG). Additionally, phenotypic evaluation of in vitro biofilm formation capacity was evaluated by Congo red agar (CRA) assay and the crystal violet staining method.
Results. The 12 isolates evaluated in this study presented the blaKPC gene and were positive for synthesizing carbapenemases in vitro. In the carbapenem class, 83.3 % isolates were resistant and 16.7 % intermediately resistant to imipenem and meropenem. Molecular analyses found that the fimA and wabG genes were detected in 75 % of isolates, while fimH and ecpA were detected in 42 % and mrkD were detected in 8.3 % (1). The CRA assay demonstrated that all isolates were slime producers and 91.7 % (11) of isolates were classified as strong and 8.3 % (1) as moderate biofilm producers by the crystal violet staining method. The optical density (OD540nm) for strong biofilm formers ranged from 0.80±0.05 to 2.47±0.28 and was 0.55±0.12 for moderate biofilm formers.
Conclusion. Our study revealed a high level of antibiotic resistance and biofilm formation in KPC isolates obtained from a hospital in Pelotas, RS, Brazil.
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Antimicrobial resistance genes and genetic characteristics of multidrug-resistant Escherichia coli in a veterinary hospital in Taiwan
More LessIntroduction. Antimicrobial resistance associated with animal hosts is easily transmitted to humans either by direct contact with resistant organisms or by transferring resistance genes into human pathogens.
Gap statement. There are limited studies on antimicrobial resistance genes and genetic elements of multidrug-resistant (MDR) Escherichia coli in veterinary hospitals in Taiwan.
Aim. The aim of this study was to investigate antimicrobial resistance genes in multidrug-resistant Escherichia coli from animals.
Methodology. Between January 2014 and August 2015, 95 multidrug-resistant Escherichia coli isolates were obtained from pigs (n=66), avians (n=18), and other animals (n=11) in a veterinary hospital in Taiwan. Susceptibility testing to 24 antimicrobial agents of 14 antimicrobial classes was performed. Antimicrobial resistance genes, integrons, and insertion sequences were analysed by polymerase chain reaction and nucleotide sequencing. Pulsed-field gel electrophoresis (PFGE), and multi-locus sequence typing were used to explore the clonal relatedness of the study isolates.
Results. Different antimicrobial resistance genes found in these isolates were associated with resistance to β-lactams, tetracycline, phenicols, sulfonamides, and aminoglycosides. Fifty-five of 95 E. coli isolates (55/95, 57.9 %) were not susceptible to extended-spectrum cephalosporins, and bla CTX-M-55 (11/55, 20.0 %) and bla CMY-2 (40/55, 72.7 %) were the most common extended-spectrum β-lactamase (ESBL) and AmpC genes, respectively. Both bla CTX-M and bla CMY-2 were present on conjugative plasmids that contained the insertion sequence ISEcp1 upstream of the bla genes. Plasmid-mediated FOX-3 β-lactamase-producing E. coli was first identified in Taiwan. Forty isolates (40/95, 42 %) with class 1 integrons showed seven resistance phenotypes. Genotyping of 95 E. coli isolates revealed 91 different XbaI pulsotypes and 52 different sequence types. PFGE analysis revealed no clonal outbreaks in our study isolates.
Conclusion. This study showed a high diversity of antimicrobial resistance genes and genotypes among MDR E. coli isolated from diseased livestock in Taiwan. To our knowledge, this is the first report of plasmid-mediated ESBL in FOX-3 β-lactamase-producing E. coli isolates in Taiwan. MDR E. coli isolates from animal origins may contaminate the environment, resulting in public health concerns, indicating that MDR isolates from animals need to be continuously investigated.
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Machine learning for identifying resistance features of Klebsiella pneumoniae using whole-genome sequence single nucleotide polymorphisms
More LessIntroduction. Klebsiella pneumoniae , a gram-negative bacterium, is a common pathogen causing nosocomial infection. The drug-resistance rate of K. pneumoniae is increasing year by year, posing a severe threat to public health worldwide. K. pneumoniae has been listed as one of the pathogens causing the global crisis of antimicrobial resistance in nosocomial infections. We need to explore the drug resistance of K. pneumoniae for clinical diagnosis. Single nucleotide polymorphisms (SNPs) are of high density and have rich genetic information in whole-genome sequencing (WGS), which can affect the structure or expression of proteins. SNPs can be used to explore mutation sites associated with bacterial resistance.
Hypothesis/Gap Statement. Machine learning methods can detect genetic features associated with the drug resistance of K. pneumoniae from whole-genome SNP data.
Aims. This work used Fast Feature Selection (FFS) and Codon Mutation Detection (CMD) machine learning methods to detect genetic features related to drug resistance of K. pneumoniae from whole-genome SNP data.
Methods. WGS data on resistance of K. pneumoniae strains to four antibiotics (tetracycline, gentamicin, imipenem, amikacin) were downloaded from the European Nucleotide Archive (ENA). Sequence alignments were performed with MUMmer 3 to complete SNP calling using K. pneumoniae HS11286 chromosome as the reference genome. The FFS algorithm was applied to feature selection of the SNP dataset. The training set was constructed based on mutation sites with mutation frequency >0.995. Based on the original SNP training set, 70% of SNPs were randomly selected from each dataset as the test set to verify the accuracy of the training results. Finally, the resistance genes were obtained by the CMD algorithm and Venny.
Results. The number of strains resistant to tetracycline, gentamicin, imipenem and amikacin was 931, 1048, 789 and 203, respectively. Machine learning algorithms were applied to the SNP training set and test set, and 28 and 23 resistance genes were predicted, respectively. The 28 resistance genes in the training set included 22 genes in the test set, which verified the accuracy of gene prediction. Among them, some genes (KPHS_35310, KPHS_18220, KPHS_35880, etc.) corresponded to known resistance genes (Eef2, lpxK, MdtC, etc). Logistic regression classifiers were established based on the identified SNPs in the training set. The area under the curves (AUCs) of the four antibiotics was 0.939, 0.950, 0.912 and 0.935, showing a strong ability to predict bacterial resistance.
Conclusion. Machine learning methods can effectively be used to predict resistance genes and associated SNPs. The FFS and CMD algorithms have wide applicability. They can be used for the drug-resistance analysis of any microorganism with genomic variation and phenotypic data. This work lays a foundation for resistance research in clinical applications.
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- Clinical Microbiology
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Clinical characteristics and prognostic risk factors of mortality in patients with interstitial lung diseases and viral infection: a retrospective cohort study
More LessIntroduction. Patients with interstitial lung disease (ILD) who subsequently develop a viral infection have high rates of morbidity and mortality.
Hypothesis/Gap Statement. Few large-scale epidemiological studies have investigated potential prognostic factors for morbidity and mortality in this patient group.
Aim. To evaluate the risk factors for morbidity and mortality in hospitalized patients with ILD and viral infection, as well as the clinical characteristics.
Methodology. This retrospective cohort study included patients with ILD who were hospitalized for a viral infection in two tertiary academic hospitals in China, between 1 January 2013 and 31 December 2019. We analysed the prevalence of comorbidities, clinical characteristics, 30 day mortality rates, and prognostic risk factors.
Results. A total of 282 patients were included; 195 and 87 were immunocompromised and immunocompetent, respectively. The most common underlying interstitial diseases were idiopathic pulmonary fibrosis (42.9 %) and connective tissue disease (36.9 %). The 30 day mortality rate was 20.6 %. During the influenza season, an increase in influenza virus (IFV) (25.7 %), respiratory syncytial virus (14.9 %) and cytomegalovirus (CMV) (11.3 %) cases was observed in the immunocompromised group. The most frequently detected virus in the immunocompetent group was IFV (44.8 %), followed by respiratory syncytial virus (11.5 %), and human rhinovirus (9.2 %). During the non-influenza season, CMV (34.4 %) was the main virus detected in the immunocompromised group. The 30 day mortality rates of non-IFV patients were higher than those of IFV patients. Older age (>60 years), respiratory failure, persistent lymphocytopenia, invasive mechanical ventilation and non-IFV virus infection were significantly associated with increased 30 day mortality.
Conclusion. Patients with ILD who develop viral infection have high rates of morbidity and mortality, which are associated with increased age (>60 years), respiratory failure, mechanical ventilation, persistent lymphocytopenia and non-IFV virus infection. These risk factors should be carefully considered when determining treatment strategies for this patient population.
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Effects of intrauterine exposure to hepatitis B virus in foetuses
More LessFoetal response to hepatitis B viral infection is still unknown. The mechanisms of persistent infection that occurs more often in mother-to-child transmission than adult transmission are also unclear. Various aspects of the environmental factors that accelerate or inhibit infection and the cytokine responses are associated with the persistence of infection. Several studies showed that the cytokine poor immune response in immaturity causes the persistence of the infection. However, some reports suggested that a mature immune response was the cause of this persistent infection. This review comprehensively summarized the reports from in vitro, in vivo as well as clinical reports regarding the responses of the foetuses of hepatitis B infected mothers to the micro-organism. The mechanism of more opportunities to be persistently infected via the mother-to-child transmission route is also summarized and discussed. Since there are limited clinical reports at this time, this review will provide evidence for future studies regarding the intrauterine infection mechanism and foetal response to hepatitis B virus to elucidate the mechanisms responsible for mother-to-child transmission. This understanding may lead to effective interventions to control mother-to-child hepatitis B infection in the future.
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Molecular mechanisms of macrolide and fluoroquinolone resistance among Korean isolates of Mycoplasma genitalium over a period of five years 2014–2019
More LessAntimicrobial resistance in Mycoplasma genitalium has become a global issue, and certain groups have a higher probability of acquiring resistant strains. Little is known about the genetic diversity and characteristics of the antimicrobial resistance-determining sites (ARDSs) of M. genitalium in the Korean population. Therefore, we examined the genetic diversity of the ARDSs of M. genitalium-positive urogenital samples obtained from Korean females (G1) and males (G2) visiting primary care clinics and DNA samples from referred males (G3) with persistent urethritis. From 2014 to 2019, 54 patients from G1, 86 patients from G2, and 68 patients from G3 were included in the study. Sanger sequencing was performed on the 2058/2059 sites in the 23S rRNA gene and quinolone resistance-determining regions (QRDRs) of M. genitalium . The rates of mutation in G1, G2, and G3 were 1.85, 5.81, and 48.53 %, respectively, for A2059G in the 23S rRNA gene (P<0.001); 1.85, 0, and 17.78 %, respectively, for M95R or I in gyrA (P<0.001); 0, 0, and 31.11 %, respectively, for D99N or G in gyrA (P<0.001); and 7.41, 16.28, and 30 %, respectively, for S83R or N or I in parC (P=0.015). A2059G significantly increased the risk of mutations at the gyrA95, gyrA99, and parC83 sites (all P<0.01). In conclusion, although the genetic diversity of the ARDSs of M. genitalium was variable among the groups, it was generally lower in isolates with macrolide resistance and higher in isolates with quinolone resistance in Korea compared with the isolates in other countries. The G3 group demonstrated increased genetic diversity at the A2059G, gyrA95, gyrA99, and parC83 sites.
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- Disease, Diagnosis and Diagnostics
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Effect of COVID-19 on vaccination coverage in Brazil
More LessDuring the COVID-19 pandemic, recommendations for maintaining physical distance, restricted mobility measures, as well as fear of mass transmission by going to health centers have significantly contributed to the general vaccination coverage, which by and large is decreasing worldwide; thus, favoring the potential re-emergence of vaccine-preventable diseases. In this study, we have used the existing data on vaccination coverage during the pre-pandemic (2019) as well as the pandemic (2020) period to evaluate the impact of coronavirus outbreaks during the vaccination drive in Brazil. Furthermore, we have accumulated data since 2015 among the different regions of the country to acquire more consistent information. The various vaccines analyzed in our study were meningococcal C conjugate, Triple antigen vaccine, 10-valent pneumococcal conjugate, and BCG; subsequently, the data were obtained from the National Disease Notification System. This study revealed that the ongoing immunization drive saw a steep decline of around 10 to 20% during the (2019–2020) pandemic period in Brazil. These results provide strong evidence towards the decreasing trends following the vaccination programs during the COVID-19 pandemic period in Brazil. Furthermore, our results also highlight the importance of adopting widespread multi-component interventions to improve vaccination uptake rates.
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- Molecular and Microbial Epidemiology
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Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015–2016
Introduction. The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that Vibrio cholerae isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon.
Gap statement. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies.
Aim. We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for V. cholerae isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines.
Methodology. A total of 139 V . cholerae O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping.
Results. We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (n=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries.
Conclusions. The genotypic relationship of the V. cholerae isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of V. cholerae genotypes in the Philippines.
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- One Health ‒ Emerging, Zoonotic and Environmental Diseases
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Sixteen cases of severe pneumonia caused by Chlamydia psittaci in South China investigated via metagenomic next-generation sequencing
Introduction. Chlamydia psittaci is an important cause of community-acquired pneumonia (CAP). The spectrum of CAP due to Chlamydia psittaci ranges from mild, self-limited to acute respiratory failure and the early identification of this disease can be challenging. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid has the potential to improve the pathogen identification in severe CAP.
Hypothesis/Gap Statement. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid has the potential to rapidly identify pathogens in severe CAP. The early identification and appropriate use of antibiotics can improve the prognosis of severe CAP caused by Chlamydia psittaci .
Aim. The aim of the study is to describe the clinical spectrum of severe psittacosis pneumonia to provide a better understanding of this disease and to demonstrate that mNGS is an effective method for pathogen detection.
Methodology. Retrospective case analysis from November 2019 to November 2020 was performed. Sixteen cases of severe psittacosis pneumonia were diagnosed through mNGS. Clinical features, laboratory findings, imaging features, treatment and outcome were summarized.
Results. Frequent symptoms included fever (16/16, 100%), dyspnoea (16/16, 100%), cough (12/16, 75%), sputum (11/16, 69%) and headache (9/16, 56%). The median leukocytosis was within the normal range, while C-reactive proteins, CK, LDH, AST, D-Dimer were significantly elevated. The feature of computed tomography included ground-glass opacity with consolidation and multiple lobar distributions. The total number of sequences of Chlamydia psittaci identified from bronchoalveolar lavage by mNGS varied from 58 to 57115. Five patients underwent noninvasive mechanical ventilation, four patients underwent high flow humidified oxygen therapy and one patient underwent invasive mechanical ventilation. Two patients had septic shock needing vasoactive medications. All of the sixteen patients experienced full recoveries.
Conclusion. The symptoms of severe CAP caused by Chlamydia psittaci were not typical while laboratory results may have some clues. The mNGS technology can early detect of psittacosis, reduce unnecessary use of antibiotics and short the course of the disease.
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Volumes and issues
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Volume 73 (2024)
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