Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infections, and a suspected outbreak of multi-drug-resistant Klebsiella pneumoniae was investigated using genomic characterisation. All K. pneumoniae bloodstream infections (BSIs) from patients in the neonatal ward (n=62), and a subset of K. pneumoniae BSI isolates (n=38) from other paediatric wards in the hospital, collected over a 4 year period were studied. After whole genome sequencing, the strain sequence types (STs), plasmid types, virulence and resistance genes were identified. One ST340 clone, part of clonal complex 258 (CC258) and an ST that drives hospital outbreaks worldwide, harbouring numerous resistance genes and plasmids, was implicated as the likely cause of the outbreak. This study contributes molecular information necessary for tracking and characterizing this important hospital pathogen in sub-Saharan Africa.

Analysis of the diagnostic accuracy of rapid antigenic tests for detection of SARS-CoV-2 in hospital outbreak situation

The reverse transcriptase polymerase chain reaction (RT-PCR) continues to be the reference diagnostic method for the confirmation of COVID-19 cases; however, rapid antigen detection tests (RADT) have recently been developed. The purpose of the study is to assess the performance of rapid antigen-based COVID-19 testing in the context of hospital outbreaks. This was an observational, cross-sectional study. The study period was from October 2020 to January 2021. The “Panbio COVID-19 AG” RADT (Abbott) was performed and TaqPath COVID-19 test RT-PCR. The samples were obtained from hospitalised patients in suspected outbreak situations at the Ramón y Cajal Hospital. A hospital outbreak was defined as the presence of 3 or more epidemiologically linked cases. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the RADT were calculated using RT-PCR as a reference. A total of 17 hospital outbreaks were detected in 11 hospital units during the study period, in which 34 RT-PCR and RADT screenings were performed. We obtained 541 samples, which were analysed with RT-PCR and a further 541 analysed with RADT. Six RADT tests gave conflicting results with the RT-PCR, 5 of them with a negative RADT and positive RT-PCR and one with positive RADT and a negative RT-PCR. The sensitivity of the RADT was 83.3% (65.3–94.4%) and the specificity was 99.8% (98.9–100%). The PPV was 96.2% (80.4–99.9%) and the NPV was 99% (97.7–99.7%). The RADT shows good diagnostic performance in patients on non-COVID-19 hospital wards, in the context of an outbreak.

Use of whole genome sequencing to investigate a cluster of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in emergency department personnel

Several recent reports have raised concern that infected co-workers may be an important source of SARS-CoV-2 acquisition by healthcare personnel. In a suspected outbreak among emergency department personnel, sequencing of SARS-CoV-2 confirmed transmission among co-workers. The suspected 6-person outbreak included 2 distinct transmission clusters and 1 unrelated infection.

Genomic surveillance, characterisation and intervention of a carbapenem-resistant Acinetobacter baumannii outbreak in critical care

Infections caused by carbapenem-resistant Acinetobacter baumannii (CR-Ab) have become increasingly prevalent in clinical settings and often result in significant morbidity and mortality due to their multidrug resistance (MDR). Here we present an integrated whole genome sequencing (WGS) response to a polymicrobial outbreak in a Brisbane hospital between 2016-2018. 28 CR-Ab (and 21 other MDR Gram negative bacilli) were collected from Intensive Care Unit and Burns Unit patients and sent for WGS with a 7-day turn-around-time in clinical reporting. All CR-Ab were sequence type (ST)1050 and within 10 single nucleotide polymorphisms (SNPs) apart, indicative of an ongoing outbreak, and distinct from historical CR-Ab isolates from the same hospital. Possible transmission routes between patients were identified on the basis of CR-Ab and K. pneumoniae SNP profiles. Continued WGS surveillance between 2016 to 2018 enabled suspected outbreak cases to be refuted, but a resurgence of the outbreak CR-Ab mid-2018 in the Burns Unit prompted additional screening. Environmental metagenomic sequencing identified the hospital plumbing as a potential source. Replacement of the plumbing and routine drain maintenance resulted in rapid resolution of the secondary outbreak and significant risk reduction with no discernable transmission in the Burns Unit since. Here we demonstrate implementation of a comprehensive WGS and metagenomics investigation that resolved a persistent CR-Ab outbreak in a critical care setting.

Genomic investigation of a suspected multi-drug resistant Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

ABSTRACTA suspected outbreak of multi-drug resistant (MDR) Klebsiella pneumoniae in a Malawian neonatal unit was investigated using whole-genome sequencing. Strain-types, virulence and resistance genes of K. pneumoniae isolated from patients from the hospital over a four-year period were identified. A MDR ST340 clone was implicated as the likely outbreak cause.

Investigation of an outbreak of suspected food poisoning in a school

Background: An outbreak investigation for food poisoning in a school of rural Maharashtra was carried out. This school had central kitchen for children staying at hostel. During monsoon season occurrence of acute gastroenteritis diseases is common and hence it important to investigate each and every suspected outbreak presenting with similar symptoms to that of acute gastroenteritis.Methods: It was a retrospective and prospective study design. All 140 children who ate food from central kitchen were interviewed and followed up. Median incubation period was obtained from the 12 children who fitted into case definition which was given by integrated diseases control program of Maharashtra. Environmental and food sampling along with laboratory investigations was done for diagnosis.Results: Total 12 children had symptoms of food poisoning. The median incubation period was around 8 hours. Gastrointestinal symptoms were the commonest reported by all the 12 children. It was found out that all the symptomatic children had eaten laddu brought from outside and stored in unhygienic conditions.Conclusions: Eating of laddu which were stored in unhygienic conditions had resulted into growth of Clostridia streptofaecalis in it causing food poisoning to children.

Genomic investigation of a suspected outbreak of Legionella pneumophila ST82 reveals undetected heterogeneity by the present gold-standard methods, Denmark, July to November 2014

Between July and November 2014, 15 community-acquired cases of Legionnaires´ disease (LD), including four with Legionella pneumophila serogroup 1 sequence type (ST) 82, were diagnosed in Northern Zealand, Denmark. An outbreak was suspected. No ST82 isolates were found in environmental samples and no external source was established. Four putative-outbreak ST82 isolates were retrospectively subjected to whole genome sequencing (WGS) followed by phylogenetic analyses with epidemiologically unrelated ST82 sequences. The four putative-outbreak ST82 sequences fell into two clades, the two clades were separated by ca 1,700 single nt polymorphisms (SNP)s when recombination regions were included but only by 12 to 21 SNPs when these were removed. A single putative-outbreak ST82 isolate sequence segregated in the first clade. The other three clustered in the second clade, where all included sequences had < 5 SNP differences between them. Intriguingly, this clade also comprised epidemiologically unrelated isolate sequences from the UK and Denmark dating back as early as 2011. The study confirms that recombination plays a major role in L. pneumophila evolution. On the other hand, strains belonging to the same ST can have only few SNP differences despite being sampled over both large timespans and geographic distances. These are two important factors to consider in outbreak investigations.