Whole-genome sequencing data-based modeling for the investigation of an outbreak of community-associated methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit in Hong Kong

Tracking Antimicrobial Resistant Organisms Timely: a workflow validation study for successive core-genome SNP-based nosocomial transmission analysis

Background and Objectives

Effective infection prevention and control (IPC) interventions in hospitals require timely information to determine the potential transmission of antimicrobial-resistant (AMR) organisms. We proposed and developed a successive core-genome SNP (cgSNP)-based phylogenetic analysis workflow, 'Tracking Antimicrobial Resistant Organisms Timely' (TAROT), using the Oxford Nanopore Technologies (ONT) sequencer for MRSA, and compared the results with those obtained using the Illumina sequencer.

Methods

We have developed a TAROT workflow for successive phylogenetic analysis using ONT data. We sequenced 34 MRSA strains isolated from Toho University Omori Medical Center using MinION (ONT) and MiSeq (Illumina). Each strain's ONT data were inputted into TAROT (TAROT-ONT), and successive cgSNP-based phylogenetic analyses were conducted. Illumina data were processed with a batched cgSNP-based phylogenetic analysis. Assembly-based analysis identified AMR genes, AMR mutations and virulence genes.

Results

MinION generated an average sequence depth of 262× for the ST8 reference genome within 3 h. TAROT-ONT successively generated 11 phylogenetic trees for 14 ST8 strains, 7 trees for 10 ST1 strains and 2 trees for 5 ST5 strains. Highly suspected transmission pairs (pairwise cgSNP< 5) were detected in trees #6 through #11 for ST8, trees #3, #5 and #7 for ST1, and tree #2 for ST5. Differences in pairwise cgSNP value between TAROT-ONT and Illumina ranged from zero to two within pairs with fewer than 20 cgSNPs using Illumina. TAROT-ONT bioinformatic analysis for each strain required 5-42 min. The identification of AMR genes, mutations and virulence genes showed high concordance between ONT and Illumina.

Conclusions

TAROT-ONT can facilitate effective IPC intervention for MRSA nosocomial transmissions by providing timely feedback through successive phylogenetic analyses based on cgSNPs.

Risk factors for colonization/infection by resistant microorganisms in outbreaks in neonatal unit-a systematic review and meta-analysis

OBJECTIVE

This study aims to evaluate risk factors for infection/colonization by resistant bacteria among patients in Neonatal Intensive Care Units (NICU).

METHODS

This systematic review is reported according to PRISMA. The search occurred by consulting the PubMed, Embase, Cochrane, SciELO, and Scopus databases. Inclusion criteria considered studies with Neonatal population admitted to the Neonatal Intensive Care Unit (P); Risk factors for resistant bacterial infection (E); No risk factors for resistant bacterial infection (C); Isolation of resistant bacteria in an outbreak (O), Observational studies (S). For Meta-Analysis, data were transformed to a logarithmic scale to directly calculate the standard error from the confidence intervals. The quality of studies was assessed Critical Appraisal Tools recommended by JBI.

RESULTS

A total of 21 articles were eligible and presented a sample size ranging from 10 to 263 newborns (a total of 1979 neonates). Six (28.6 %) studies evaluated infection, five (23.8) evaluated colonization, and 10 (47.6 %) evaluated colonization and infection, covering Gram-positive (n = 8; 38 %) and Gram-negative (n = 13; 62 %) bacteria. In the meta-analysis, the use of venous access (OR: 1.58; 95 %CI 1.14-2.20), mechanical ventilation (OR: 7.55 95 %CI 4.27-13.36), and parenteral nutrition (OR: 4.79; 95 %CI 2.23-10.29) increased the chance of colonization/infection by multiresistant microorganisms. The included studies were considered as having adequate quality.

CONCLUSION

The main risk factors in outbreaks of infection/colonization by resistant microorganisms in Neonatal Units are the use of invasive devices and parenteral nutrition, which leads to the identification of newborns at risk, targeting the development of preventive measures.

Distribution of Antimicrobial Resistance and Biofilm Production Genes in the Genomic Sequences of S. aureus: A Global In Silico Analysis

Background:Staphylococcus aureus constitutes a significant public health threat due to its exceptional adaptability, antimicrobial resistance (AMR), and capacity to form biofilms, all of which facilitate its persistence in clinical and environmental settings. Methods: This study undertook an extensive in silico analysis of 44,069 S. aureus genomic sequences acquired from the NCBI database to assess the global distribution of biofilm-associated and resistance-associated genes. The genomes were categorized into human clinical and environmental groups, with clinical samples representing a predominant 96%. Results: The analysis revealed notable regional discrepancies in sequencing efforts, with Europe and North America contributing 76% of the genomes. Key findings include the high prevalence of the ica locus, which is associated with biofilm formation, and its robust correlation with other genes, such as sasG, which was exclusively linked to SCCmec type IIa. The AMR gene analysis revealed substantial genetic diversity within environmental samples, with genes like vga(E) and erm being identified as particularly prominent. The clonal complex analysis revealed ST8 (USA300) and ST5 as the predominant types in human clinical isolates, while ST398 and ST59 were most frequently observed in environmental isolates. SCCmec type IV was globally prevalent, with subtype Iva being strongly associated with ST8 in North America and subtype IVh with ST239 in Europe. Conclusions: These findings underscore the dynamic evolution of S. aureus via mobile genetic elements and highlight the necessity for standardized metadata in public genomic databases to improve surveillance efforts. Furthermore, they reinforce the critical need for a One Health approach in monitoring S. aureus evolution, particularly concerning the co-dissemination of biofilm and resistance genes across various ecological niches.

Isolation of community-associated methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 30 from house rats (Rattus tanezumi) in Hong Kong

Methicillin-resistant Staphylococcus aureus (MRSA) is of major public health concern due to its resistance to multiple antibiotics. This resistance has been observed in various settings, including hospitals and communities, and has been detected in both animals and humans. Although peridomestic rat species (Rattus spp.) are well described reservoirs of several human pathogens and antimicrobial resistant bacteria, little is known about their role in MRSA epidemiology. In order to investigate whether Rattus spp. in Hong Kong are potential carriers of MRSA, 221 rats were caught from various ecological areas and nasopharyngeal samples were cultured on MRSA selective media. Genotypic characteristics of MRSA were confirmed by whole genome sequencing. Two clonal sequence type (ST) 30 MRSA isolates, harbouring mecA on staphylococcal chromosome cassette (SCC) mec type IVc, were cultured from two house rats (Rattus tanezumi) caught in two densely populated urban areas. To the best of the authors' knowledge, this is the first detection of community-associated (CA)-MRSA strain ST30 SCCmec IVc in peridomestic rodents in Hong Kong and globally. Our finding indicates that house rats can be carriers of MRSA strains that are widely distributed in the community.

Outbreaks in the Neonatal Intensive Care Unit: Description and Management

Healthcare settings, especially intensive care units, can provide an ideal environment for the transmission of pathogens and the onset of outbreaks. Many factors can contribute to the onset of an epidemic in a neonatal intensive care unit (NICU), including neonates' vulnerability to healthcare-associated infections, especially for those born preterm; facility design; frequent invasive procedures; and frequent contact with healthcare personnel. Outbreaks in NICUs are one of the most relevant problems because they are often caused by multidrug-resistant organisms associated with increased mortality and morbidity. The prompt identification of an outbreak, the subsequent investigation to identify the source of infection, the risk factors, the reinforcement of routine infection control measures, and the implementation of additional control measures are essential elements to contain an epidemic.

Linking preterm infant gut microbiota to nasograstric enteral feeding tubes: exploring potential interactions and microbial strain transmission

Introduction

Preterm birth is a growing problem worldwide. Staying at a neonatal intensive care unit (NICU) after birth is critical for the survival of preterm infants whose feeding often requires the use of nasogastric enteral feeding tubes (NEFT). These can be colonized by hospital-associated pathobionts that can access the gut of the preterm infants through this route. Since the gut microbiota is the most impactful factor on maturation of the immune system, any disturbance in this may condition their health. Therefore, the aim of this study is to assess the impact of NEFT-associated microbial communities on the establishment of the gut microbiota in preterm infants.

Material and methods

A metataxonomic analysis of fecal and NEFT-related samples obtained during the first 2 weeks of life of preterm infants was performed. The potential sharing of strains isolated from the same set of samples of bacterial species involved in NICU's outbreaks, was assessed by Random Amplification of Polymorphic DNA (RAPD) genotyping.

Results

In the samples taken 48 h after birth (NEFT-1 and Me/F1), Staphylococcus spp. was the most abundant genera (62% and 14%, respectively) and it was latter displaced to 5.5% and 0.45%, respectively by Enterobacteriaceae. Significant differences in beta diversity were detected in NEFT and fecal samples taken at day 17 after birth (NEFT-3 and F3) (p = 0.003 and p = 0.024, respectively). Significant positive correlations were found between the most relevant genera detected in NEFT-3 and F3. 28% of the patients shared at least one RAPD-PCR profile in fecal and NEFT samples and 11% of the total profiles were found at least once simultaneously in NEFT and fecal samples from the same patient.

Conclusion

The results indicate a parallel bacterial colonization of the gut of preterm neonates and the NEFTs used for feeding, potentially involving strain sharing between these niches. Moreover, the same bacterial RAPD profiles were found in neonates hospitalized in different boxes, suggesting a microbial transference within the NICU environment. This study may assist clinical staff in implementing best practices to mitigate the spread of pathogens that could threaten the health of preterm infants.

Comparative Genomic Analysis of Staphylococcal Cassette Chromosome mec Type V Staphylococcus aureus Strains and Estimation of the Emergence of SCCmec V Clinical Isolates in Korea

Background

Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains.

Methods

Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Ranger-dtl was applied to 818 SCCmec V strains using publicly available whole-genome data.

Results

The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000-2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors.

Conclusions

Most Korean SCCmec V strains may have emerged during 2000-2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.

Whole-genome sequencing links cases dispersed in time, place, and person while supporting healthcare worker management in an outbreak of Panton-Valentine leucocidin meticillin-resistant Staphylococcus aureus; and a review of literature

This is a report on an outbreak of Panton-Valentine leucocidin-producing meticillin-resistant Staphylococcus aureus (PVL-MRSA) in an intensive care unit (ICU) during the COVID-19 pandemic that affected seven patients and a member of staff. Six patients were infected over a period of ten months on ICU by the same strain of PVL-MRSA, and a historic case identified outside of the ICU. All cases were linked to a healthcare worker (HCW) who was colonized with the organism. Failed topical decolonization therapy, without systemic antibiotic therapy, resulted in ongoing transmission and one preventable acquisition of PVL-MRSA. The outbreak identifies the support that may be needed for HCWs implicated in outbreaks. It also demonstrates the role of whole-genome sequencing in identifying dispersed and historic cases related to the outbreak, which in turn aids decision-making in outbreak management and HCW support. This report also includes a review of literature of PVL-MRSA-associated outbreaks in healthcare and highlights the need for review of current national guidance in the management of HCWs' decolonization regimen and return-to-work recommendations in such outbreaks.

Comprehensive investigation of antibiotic resistance gene content in cfiA-harboring Bacteroides fragilis isolates of human and animal origins by whole genome sequencing

INTRODUCTION

The emergence of multidrug resistance in Bacteroides fragilis, especially the phylogenetic lineage carrying the carbapenemase gene cfiA, represents an increasing threat to human health. However, knowledge on the diversity of the multidrug-resistant strains and the genetic elements carrying the antibiotic resistance genes (ARGs) remains limited.

AIM

The objective of the study was to describe the resistome in cfiA-positive B. fragilis.

METHODS

A collection of cfiA-positive B. fragilis from diverse human (8 bacteremias, 15 wound infections) and animal (2 chickens, 2 pigs, 6 dogs, 3 cats) sources in Hong Kong, 2015-2017 was analysed by whole genome sequencing.

RESULTS

In the 36 isolates, 13 distinct ARGs (total number 83, median 2, range 0-7 per isolate) other than cfiA were detected. ARGs encoding resistance to aminoglycosides, β-lactams, macrolides, sulphonamides and tetracyclines were carried by CTn341-like, CTnHyb-like, Tn5220-like, Tn4555-like and Tn613-like transposons and were detected in phylogenetically diverse isolates of different host sources. Only few ARGs encoding resistance to metronidazole and tetracyclines were localized on plasmids. In two chicken isolates, a novel transposon (designated as Tn6994) was found to be involved in the dissemination of multiple ARGs mediating resistance to multiple antibiotics, including metronidazole and linezolid that are critically important for treatment of anaerobic infections. In mating experiments, Tn6994 and the associated phenotypic resistance could be transferred to Bacteroides nordii recipient.

CONCLUSION

This study illustrates the importance of transposons in the dissemination of ARGs in the cfiA-positive division of B. fragilis. One Health approach is necessary to track the dissemination of ARGs.

Gastrointestinal colonization of methicillin-resistant Staphylococcus aureus: an unrecognized burden in the hospital infection control

The incidence, risk factors, outcomes, and genomic relatedness of patients with newly diagnosed gastrointestinal colonization of meticillin-resistant Staphylococcus aureus (MRSA) were analyzed epidemiologically and genetically by whole genome sequencing (WGS) in a hospital network in Hong Kong. Between 1 October 2015 and 31 December 2018, 919 (2.7%) of 34,667 patients had newly diagnosed gastrointestinal MRSA colonization by admission screening. The incidence was 0.67±0.32 per 1,000-patient-days-per-quarter. Including patients with gastrointestinal MRSA colonization, the overall burden of MRSA increased by 59.2% (from 1.13±0.13 to 1.80±0.36 case per 1,000-patient-days-per-quarter), with an addition of MRSA 4,727 patient-days during the study period. Patients referred from residential care home for the elderly [odds ratio (95% confidential interval): 4.18 (3.50-4.99), p<0.001], with history of hospitalization in the past 6 months [1.90 (1.56-2.30), p<0.001], and consumption of fluoroquinolones [1.76 (1.34-2.30), p<0.001], cephalosporins [1.61 (1.11-2.31), p=0.011], and proton pump inhibitors [1.31 (1.10-1.56), p=0.002] in the preceding 6 months were found to be independent risk factors by multivariable analysis in the case-control analysis. The median survival of case was significantly shorter than control (860 vs 1507 days, p<0.001). 127 (13.8%) of 919 patients developed symptomatic MRSA infection in 112 days (median, range: 2-712 days). Of 19 patients with paired MRSA faecal and blood culture isolates subjected to WGS, clonality was found in 16 (84.2%) pairs of MRSA isolates. MRSA ST45 constituted 44.7% (17/38) of MRSA isolates. Gastrointestinal MRSA colonization may contribute to adverse clinical outcomes and pose an unrecognized burden to the hospital infection control.

Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo

Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo. © 2021 The Authors. Basic Protocol 1: First steps with TransPhylo Basic Protocol 2: Simulation of outbreak data Basic Protocol 3: Inference of transmission Basic Protocol 4: Exploring the results of inference.

Prevalence of MRSA nasal carriage among pregnant women in Copenhagen

Background

Methicillin resistant Staphylococcus aureus (MRSA) frequently causes outbreaks in neonatal intensive care units (NICUs). It is believed that MRSA predominantly enters the NICU with MRSA colonized parents. In Denmark, 27 MRSA NICU outbreaks have been registered between 2008 and 2019.

Aim

The aim of this study was to determine the prevalence of MRSA nasal carriage in pregnant women in Copenhagen and to clarify if MRSA screening during pregnancy could add to the prevention of NICU outbreaks.

Methods

All pregnant women 18 years or older were offered MRSA nasal screening at their first midwife visit between 13 and 20 weeks of gestation.

Results

1778 pregnant women were included, two (0.11%) carried MRSA in the nose.

Conclusion

Infants of the two MRSA positive women were not admitted to a NICU and therefore the screening had no impact on NICU outbreaks. The low prevalence of MRSA found in this study does not justify MRSA screening of all pregnant women in Denmark.

Phenotypic and Molecular Characteristics of Community-Associated Staphylococcus aureus Infection in Neonates

Background

Staphylococcus aureus is an important human pathogen causing a wide variety of diseases ranging from mild skin infections to life-threatening bacteremia. This study aimed to provide insight into the phenotype-genotype characteristics of S. aureus isolated from neonates.

Methods

A hospital-based retrospective study was conducted to recruit neonatal patients with community-associated S. aureus infection. All 92 S. aureus clinical isolates were tested for antimicrobial susceptibility, resistance genes, virulence genes, and multilocus sequence typing.

Results

A total of 92 S. aureus isolates were included in this study, including 29 (31.5%) MRSA isolates. Most S. aureus isolates were susceptible to gentamicin, and most methicillin-resistant S. aureus (MRSA) isolates were susceptible to vancomycin and linezolid. The predominant S. aureus genotypes were CC188 (ST188), CC59 (ST338), CC5 (ST5), CC88 (ST8), and CC6 (ST6), with CC59 (ST338) as the most prevalent MRSA. We observed a significantly corresponding relationship between clonal complexes and resistance patterns (such as CC45/CC59/CC121/CC630 associated with multidrug resistance) or the number of virulence genes (such as CC1/CC5/CC45/CC59/CC88 associated with harboring 5-7 virulence genes, and CC22/CC25/CC121 associated with carrying 8-13 genes). Moreover, both univariate and multivariate analyses indicated that invasive S. aureus isolates were significantly associated with resistance to several classes of antibiotics and carrying specific virulence factors.

Conclusion

Our findings provide insight into phenotype-genotype characteristics for S. aureus isolates so as to provide new ideas for differentiating potential genetic backgrounds and monitoring new epidemiologic trends.

A persistent recurring cluster of meticillin-resistant Staphylococcus aureus (MRSA) colonizations in a special care baby unit: a matched case-control study

BACKGROUND

Between August 2016 and November 2019, a cluster of babies colonized with meticillin-resistant Staphylococcus aureus (MRSA) was reported in a special care baby unit in northern England.

AIM

A case-control study was performed to identify the source and prevent further cases.

METHODS

Cases were admitted neonates colonized or infected with MRSA (spa type t316). A retrospective case-control study was performed with two matched controls per case. Exposures were determined by medical record review. Cases were compared with controls using conditional logistic regression. Environmental investigations and staff screening were undertaken.

FINDINGS

Thirty-one colonized cases were identified across the 3-year period, with no infections reported. Thirteen of the 31 cases were sequenced and were within a cluster of 25 single nucleotide polymorphisms, consistent with exposure to a common source over a prolonged period. Most MRSA cases had a prior negative screen (N=22, 71%). Environmental sampling and staff screening were performed on several occasions. In the analytical study, 31 cases were compared with 62 controls. One ward location and one healthcare worker were identified as significant exposures in the multi-variable analysis.

CONCLUSIONS

Due to the sporadic nature of the colonizations, it was hypothesized that MRSA was being introduced intermittently, likely by a colonized healthcare worker, with possible transmission between infants also occurring within each temporal cluster. It is recommended that transiently colonized healthcare workers should be considered as a source of MRSA during outbreaks. This study highlights the importance of analytic epidemiological studies in persistent outbreaks of MRSA.

The Genomic Context for the Evolution and Transmission of Community-Associated Staphylococcus aureus ST59 Through the Food Chain

Sequence type 59 (ST59) is a predominant clonal lineage of community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) in Asia. Despite its increasing clinical relevance in China, the evolution and geographic expansion of ST59 has been relatively uncared for. Previous study has shown that ST59 was the predominant clone in food-related MRSA in China. This study compared the genomes of 87 clonal complex (CC) 59 S. aureus isolates sourced from food chain and infection cases to reconstruct the molecular evolution and geographical spread of ST59. Accordingly, three major sub-clades of ST59 were identified and these did not correlate with isolation source or location. Phylogenetic analysis estimated that ST59 in mainland China diverged from a most common recent ancestor around 1974, and most of the cases of cross-country transmission occurred between 1987 and 2000. Notably, two recent events of cross-country transmission through the food chain were observed, the isolates from these events diverged within relatively short time intervals. These isolates also showed high similarity in terms of their core genome, accessory genes, and antibiotic resistance patterns. These findings provide a valuable insight into the potential route of ST59 expansion in China and indicate a need for robust food chain surveillance to prevent the spread of this pathogen.

A comparative genomic analysis between methicillin-resistant Staphylococcus aureus strains of hospital acquired and community infections in Yunnan province of China

BACKGROUND

Currently, Staphylococcus aureus is one of the most important pathogens worldwide, especially for methicillin-resistant S. aureus (MRSA) infection. However, few reports referred to patients' MRSA infections in Yunnan province, southwest China.

METHODS

In this study, we selected representative MRSA strains from patients' systemic surveillance in Yunnan province of China, performed the genomic sequencing and compared their features, together with some food derived strains.

RESULTS

Among sixty selective isolates, forty strains were isolated from patients, and twenty isolated from food. Among the patients' strains, sixteen were recognized as community-acquired (CA), compared with 24 for hospital-acquired (HA). ST6-t701, ST59-t437 and ST239-t030 were the three major genotype profiles. ST6-t701 was predominated in food strains, while ST59-t437 and ST239-t030 were the primary clones in patients. The clinical features between CA and HA-MRSA of patients were statistical different. Compared the antibiotic resistant results between patients and food indicated that higher antibiotic resistant rates were found in patients' strains. Totally, the average genome sizes of 60 isolates were 2.79 ± 0.05 Mbp, with GC content 33% and 84.50 ± 0.20% of coding rate. The core genomes of these isolates were 1593 genes. Phylogenetic analysis based on pan-genome and SNP of strains showed that five clustering groups were generated. Clustering ST239-t030 contained all the HA-MRSA cases in this study; clustering ST6-t701 referred to food and CA-MRSA infections in community; clustering ST59-t437 showed the heterogeneity for provoking different clinical diseases in both community and hospital. Phylogenetic tree, incorporating 24 isolates from different regions, indicated ST239-t030 strains in this study were more closely related to T0131 isolate from Tianjin, China, belonged to 'Turkish clade' from Eastern Europe; two groups of ST59-t437 clones of MRSA in Yunnan province were generated, belonged to the 'Asian-Pacific' clone (AP) and 'Taiwan' clone (TW) respectively.

CONCLUSIONS

ST239-t030, ST59-t437 and ST6-t701 were the three major MRSA clones in Yunnan province of China. ST239-t030 clonal Yunnan isolates demonstrated the local endemic of clone establishment for a number of years, whereas ST59-t437 strains revealed the multi-origins of this clone. In general, genomic study on epidemic clones of MRSA in southwest China provided the features and evolution of this pathogen.