An outbreak of Klebsiella pneumoniae late-onset sepsis in a neonatal intensive care unit in Guatemala

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality

BACKGROUND

Captive koala breeding programmes are essential for long-term species management. However, breeding efficacy is frequently impacted by high neonatal mortality rates in otherwise healthy females. Loss of pouch young typically occurs during early lactation without prior complications during parturition and is often attributed to bacterial infection. While these infections are thought to originate from the maternal pouch, little is known about the microbial composition of koala pouches. As such, we characterised the koala pouch microbiome across the reproductive cycle and identified bacteria associated with mortality in a cohort of 39 captive animals housed at two facilities.

RESULTS

Using 16S rRNA gene amplicon sequencing, we observed significant changes in pouch bacterial composition and diversity between reproductive time points, with the lowest diversity observed following parturition (Shannon entropy - 2.46). Of the 39 koalas initially sampled, 17 were successfully bred, after which seven animals lost pouch young (overall mortality rate - 41.18%). Compared to successful breeder pouches, which were largely dominated by Muribaculaceae (phylum - Bacteroidetes), unsuccessful breeder pouches exhibited persistent Enterobacteriaceae (phylum - Proteobacteria) dominance from early lactation until mortality occurred. We identified two species, Pluralibacter gergoviae and Klebsiella pneumoniae, which were associated with poor reproductive outcomes. In vitro antibiotic susceptibility testing identified resistance in both isolates to several antibiotics commonly used in koalas, with the former being multidrug resistant.

CONCLUSIONS

This study represents the first cultivation-independent characterisation of the koala pouch microbiota, and the first such investigation in marsupials associated with reproductive outcomes. Overall, our findings provide evidence that overgrowth of pathogenic organisms in the pouch during early development is associated with neonatal mortality in captive koalas. Our identification of previously unreported, multidrug resistant P. gergoviae strains linked to mortality also underscores the need for improved screening and monitoring procedures aimed at minimising neonatal mortality in future. Video Abstract.

Infection prevention and care bundles addressing health care-associated infections in neonatal care in low-middle income countries: a scoping review

BACKGROUND

Health care-associated infections (HCAI) in neonatal units in low- and middle-income countries (LMIC) are a major cause of mortality. This scoping review aimed to synthesise published literature on infection prevention and care bundles addressing neonatal HCAI in LMICs and to construct a Classification Framework for their components (elements).

METHODS

Five electronic databases were searched between January 2001 and July 2020. A mixed-methods approach was applied: qualitative content analysis was used to build a classification framework to categorise bundle elements and the contents of the classification groups were then described quantitatively.

FINDINGS

3619 records were screened, with 44 eligible studies identified. The bundle element Classification Framework created involved: (1) Primary prevention, (2) Detection, (3) Case management, and Implementation (3 + I). The 44 studies included 56 care bundles with 295 elements that were then classified. Primary prevention elements (128, 43%) predominated of which 71 (55%) focused on central line catheters and mechanical ventilators. Only 12 elements (4%) were related to detection. A further 75 (25%) elements addressed case management and 66 (88%) of these aimed at outbreak control.

INTERPRETATION

The 3 + I Classification Framework was a feasible approach to reporting and synthesising research for infection-relevant bundled interventions in neonatal units. A shift towards the use in infection prevention and care bundles of primary prevention elements focused on the neonate and on commonly used hospital devices in LMIC (e.g., self-inflating bags, suctioning equipment) would be valuable to reduce HCAI transmission. Detection elements were a major gap.

FUNDING

This work was made possible in part by the John D. and Catherine T. MacArthur Foundation, the Bill & Melinda Gates Foundation, ELMA Philanthropies, The Children's Investment Fund Foundation UK, The Lemelson Foundation, and the Ting Tsung and Wei Fong Chao Foundation under agreements to William Marsh Rice University. The project leading to these results has also received the support of a fellowship from the "la Caixa" Foundation (ID 100010434). The fellowship code is LCF/BQ/EU19/11710040. EJAF is an Academic Clinical Fellow whose salary is funded by the UK National Institute for Health Research (NIHR). NES receives a Research Training Program Scholarship (Australian Commonwealth Government).

Antimicrobial Resistance Trends at a Pediatric Hospital in Guatemala City, 2005-2019

Antimicrobial resistance (AMR) is increasing worldwide. We analyzed AMR rates for bacterial species identified from pediatric blood cultures between 2005 and 2019 at a single institution in Guatemala. We found significantly increased rates in Gram-negative resistance, with a high prevalence of carbapenem-resistant Acinetobacter and Klebsiella harboring the New Delhi metallo-beta-lactamase gene.

Draft genome sequence of an extensively drug-resistant neonatal Klebsiella pneumoniae isolate harbouring multiple plasmids contributing to antibiotic resistance

OBJECTIVES

Klebsiella pneumoniae is a notorious nosocomial pathogen that has become a significant cause of neonatal infections causing morbidity and mortality. A multidrug-resistant K. pneumoniae isolate (K184) was isolated from a 5-day-old infant admitted to the neonatal intensive care unit of a local hospital in Rawalpindi, Pakistan. Whole-genome analysis of the isolated strain was performed to gain a better understanding of the genetic basis of antimicrobial resistance and virulence determinants.

METHODS

K. pneumoniae isolate K184 was sequenced on an Illumina HiSeq 2500 platform. The genome was assembled using SPAdes with 30× coverage and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.4.3. Characterisation of the strain was performed using MLST 2.0 server. Plasmids, antimicrobial resistance determinants and virulence factors were identified using PlasmidFinder v.2.0, the Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors Database (VFDB), respectively.

RESULTS

Neonatal K. pneumoniae isolate K184 has a considerably large genome with a size of 6,686,067 bp and a GC content of 55.6%. The isolate possesses three plasmids actively contributing to antimicrobial resistance, which classifies it as heavily loaded genome, along with three prophage regions. With 15 antimicrobial resistance determinants and various virulence factors, the neonatal isolate belongs to ST2096.

CONCLUSION

The genome of neonatal isolate K184 studied here provides an insight into antibiotic resistance and virulence determinants. This draft genome can be used to compare antimicrobial-resistant K. pneumoniae strains isolated from the neonatal population.

Bottlenecks and barriers to effective coverage of early childhood health and development interventions in Guatemala: A scoping review

OBJECTIVES

To identify bottlenecks and barriers to effective coverage by Early Childhood Health and Development (ECHD) interventions in Guatemala.

METHODS

A scoping review of more than 100 peer-reviewed articles, grey literature, and other academic publications was conducted. Articles published from 2005-2019 were considered. Results were analyzed using the Tanahashi model of effective coverage that categorizes coverage by five domains: availability, accessibility, acceptability, contact, and effective coverage.

RESULTS

A total of 103 articles were identified, addressing 337 bottlenecks and barriers to effective coverage by ECHD interventions in Guatemala. Most occurred along the acceptability dimension (35.9%). The findings revealed four opportunity spaces: (i) strong political interest and commitment (opportunity for leadership); (ii) vibrant community health networks (opportunity for leverage); (iii) availability of promising evidence-based projects and interventions (opportunity for scale-up); and (iv) strong agency presence (opportunity for collaboration).

CONCLUSIONS

Most bottlenecks and barriers to ECHD interventions in Guatemala occur around acceptability, followed by accessibility and availability. There is considerable potential for national leadership, leverage, scale-up, and collaboration of ongoing efforts in the country. These results may be used to inform future research and policymaking. The Tanahashi approach is an effective lens of analysis that can be applied to other countries, geographic areas, and contexts in future studies.

Differences in clinical characteristics of early- and late-onset neonatal sepsis caused by Klebsiella pneumoniae

To identify differences in the clinical characteristics of early- and late-onset sepsis (EOS and LOS) caused by Klebsiella pneumoniae (K. pneumoniae) and to describe the risk factors for multidrug-resistant K. pneumoniae (MDR-KP) infection. Infants with K. pneumoniae-induced sepsis who were admitted to a children's Hospital between Jan 2000 and Dec 2019 were included. All infants were divided into EOS and LOS groups, as well as MDR-KP and non-MDR-KP groups. Demographics, clinical characteristics, and risk factors were compared between the two groups. One hundred eighty infants (66 with EOS and 114 with LOS) were further analyzed, accounting for 36.8% of sepsis cases caused by MDR-KP. The frequency of respiratory failure, bronchopulmonary dysplasia, and intraventricular hemorrhage were more common in the LOS group and a higher rate of acute respiratory distress syndrome was more common in infants in the EOS group (P < 0.05). K. pneumoniae showed a low sensitivity to penicillin, beta-lactams and cephalosporins, and it showed a high sensitivity to levofloxacin, ciprofloxacin, and amikacin. Prematurity, low birth weight, longer antibiotic exposure time, long duration of peripheral catheter insertion, long mechanical ventilation time, and long parenteral nutrition time were associated with an increased rate of MDR-KP infection by univariate analysis (P < 0.05). The regression analysis identified a long antibiotic exposure time (OR = 1.37, 95% CI: 1.01-1.89) and long parenteral nutrition time (OR = 1.39, 95% CI: 1.01-1.89) as independent risk factors for a MDR-KP infection, and a greater gestational age and birth weight were associated with a lower risk of MDR-KP infection (OR = 0.57, 95% CI: 0.40-0.79). LOS caused by K. pneumoniae may lead to a higher frequency of complications. The risk factors for MDR-KP infection were longer duration of antibiotic exposure and parenteral nutrition. A greater gestational age and larger birth weight may decrease the risk of MDR-KP infection.

Molecular characterization of novel sequence type of carbapenem-resistant New Delhi metallo-β-lactamase-1-producing Klebsiella pneumoniae in the neonatal intensive care unit of an Indian hospital

Emergence of multi-drug resistance, especially carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major threat to public health. The aim of this study was to characterize CRKP isolates from infants admitted to the Neonatal Intensive Care Unit (NICU) to find the clonal outbreak of New Delhi metallo-β-lactamase (NDM) producers. In this study 17 CRKP isolates were analysed. Antimicrobial susceptibility of the isolates was determined by the disc diffusion and micro-dilution method. Carba-NP test and double-disk synergy test (DDST) were performed for the detection of carbapenemase and metallo-β-lactamase-producing K. pneumoniae. Antibiotic-resistant markers were detected by polymerase chain reaction (PCR) followed by sequencing. Clonal relatedness of the isolates was checked by multi-locus sequence typing. Conjugation experiments were performed to determine the transferability of the plasmids. All 17 CKRP isolates were found to carry bla_NDM (13 bla_NDM-1, 1 bla_NDM-4 and 3 bla_NDM-5), seven isolates carried bla_OXA-48, 13 isolates had bla_CTX-M-15, seven isolates carried bla_CMY-1 and five isolates were found to carry bla_SHV-1 on conjugative plasmids of different types (IncFIA, IncFIB, IncFIIAs, IncFIC, IncA/C, IncF, IncK, IncX, IncW and IncY). Of six different sequence types (STs) identified, ST3344 was detected as a novel ST in two K. pneumoniae isolates. Genetic environment analysis revealed ISAba125 and bleomycin genes flanking to all bla_NDM variants. This is the first report of novel ST3344 in two NDM-1-producing K. pneumoniae isolates from neonates admitted to the NICU of a North Indian Hospital. This study is provides understanding of the genetic features of this newly emerged strain type.

Neonatal Sepsis in Haiti

Infections (including sepsis, meningitis, pneumonia and tetanus) stand as a major contributor to neonatal mortality in Haiti (22%). Infants acquire bacteria that cause neonatal sepsis directly from the mother's blood, skin or vaginal tract either before or during delivery. Nosocomial and environmental pathogens introduce further risk after delivery. The absence of cohesive medical systems and methods for collecting information limits the available data in countries such as Haiti. This study seeks to add more information on the burden of severe bacterial infections and their etiology in neonates of Haiti. Researchers conducted a secondary retrospective analysis of a de-identified database from the Neonatal Intensive Care Unit (NICU) at Nos Petit Frères et Soeurs-St. Damien Hospital (NPFS-SDH). Records from 1292 neonates admitted to the NICU at NPFS-SDH in Port-au-Prince Haiti from 2013 to 2015 were reviewed. Sepsis accounted for 708 of 1292 (54.8%) of all admissions to the NICU. Infants admitted for sepsis had a mortality rate of 23% (163 of 708 infants admitted for sepsis). The most common organism cultured was Streptococcus agalactiae, followed by Klebsiella pneumoniae, Pseudomonas aeroginusa, Enterobacter aerogenes, Staphylococcus aureus and Proteus mirabillis Failure to order or obtain a culture was associated with an increased fatality (odds ratio 2.4) for infants with sepsis. Resistance should be a concern when treating empirically.

Lack of evidence for the efficacy of enhanced surveillance compared to other specific interventions to control neonatal healthcare-associated infection outbreaks

Background

Despite current prevention efforts, outbreaks of healthcare-associated infections in neonatal units remain high globally, with a considerable burden of mortality and morbidity.

Methods

We searched Medline, Cochrane Library and Outbreak database to identify studies of neonatal healthcare-associated outbreaks between 2005 and 2015 that described interventions to control outbreaks. All studies were evaluated using the ORION guidance.

Results

Thirty studies were identified including 17 102 infants of whom 664 (3.9%) became infected. No single intervention was identified that reduced duration or mortality. Studies that introduced multiple interventions had significantly reduced case fatality ratio and outbreak duration compared to those that used basic surveillance only. Low and low-middle income countries reported the fewest interventions to control outbreaks and these studies were also associated with higher mortality than that found in middle and high income countries.

Conclusions

Systematic reporting and formal evaluation of interventions used to reduce healthcare-associated neonatal infection outbreaks is key to identifying containment strategies worldwide.

blaOXA-48 carrying clonal colistin resistant-carbapenem resistant Klebsiella pneumoniae in neonate intensive care unit, India

Bacteria resistant to colistin, a last resort antibiotic reflect the pre-antibiotic era. In this study, colistin resistance carbapenem-resistant K. pneumoniae (COL^R- CRKP) strains from neonate's intensive care unit were evaluated. Molecular analysis showed that all the four colistin resistant K. pneumoniae isolates were clonally related with strong biofilm formation ability and harbored bla_SHV-34 and bla_OXA-48 genes. Our result suggested the need of proper surveillance and adequate infection control to limiting the spread of these organisms.

Clinical and Molecular Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Klebsiella spp.: A Systematic Review and Meta-Analyses

Healthcare-related infections caused by extended-spectrum beta-lactamase (ESBL)-producing Klebsiella spp. are of major concern. To control transmission, deep understanding of the transmission mechanisms is needed. This systematic review aimed to identify risk factors and sources, clonal relatedness using molecular techniques, and the most effective control strategies for ESBL-producing Klebsiella spp. A systematic search of PubMed, Embase, and Outbreak Database was performed. We identified 2771 articles from November 25th, 1960 until April 7th, 2014 of which 148 were included in the systematic review and 23 in a random-effects meta-analysis study. The random-effects meta-analyses showed that underlying disease or condition (odds ratio [OR] = 6.25; 95% confidence interval [CI] = 2.85 to 13.66) generated the highest pooled estimate. ESBL-producing Klebsiella spp. were spread through person-to-person contact and via sources in the environment; we identified both monoclonal and polyclonal presence. Multi-faceted interventions are needed to prevent transmission of ESBL-producing Klebsiella spp.

Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness

We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a "commensal lifestyle." However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.

IMPORTANCE

During critical illness, the normal gut microbiota becomes disrupted in response to host physiologic stress and antibiotic treatment. Here we demonstrate that the community structure of the gut microbiota during prolonged critical illness is dramatically changed such that in many cases only two-member pathogen communities remain. Most of these ultra-low-membership communities display low virulence when grouped together (i.e., a commensal lifestyle); individually, however, they can express highly harmful behaviors (i.e., a pathogenic lifestyle). The commensal lifestyle of the whole community can be shifted to a pathogenic one in response to host factors such as opioids that are released during physiologic stress and critical illness. This shift can be prevented by using compounds such as Pi-PEG15-20 that interrupt bacterial virulence expression. Taking the data together, this report characterizes the plasticity seen with respect to the choice between a commensal lifestyle and a pathogenic lifestyle among ultra-low-diversity pathogen communities that predominate in the gut during critical illness and offers novel strategies for prevention of sepsis.

Two outbreaks of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit

BACKGROUND

In the present study, two epidemic episodes of extended spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae in the neonatal intensive care unit (NICU) were evaluated.

METHODS

Routine and surveillance culture samples were taken from seven neonates with signs of infection in the NICU of Selcuk University Faculty of Medicine between 10 March and 25 April 2011, and between 11 June and 30 September 2011.

RESULTS

ESBL-producing K. pneumoniae strains were isolated in six different samples (one wound, one blood, and four cerebrospinal fluid cultures) of the three neonates in the first episode and in 11 different samples (seven blood and four cerebrospinal fluid cultures) of the four neonates in the second episode. ESBL-producing K. pneumoniae was isolated from inguinal, axillar region, and stool samples of the nine colonized neonates in the second episode. It was determined on pulse field gel electrophoresis that all strains originated from two clones.

CONCLUSIONS

The deficiencies in the infection control measures in an NICU may transform into an epidemic rapidly. Therefore, periodic training, observation, and monitoring of compliance are important.

Spatial and temporal analyses to investigate infectious disease transmission within healthcare settings

Background

Healthcare-associated infections (HCAIs) cause significant morbidity and mortality worldwide, and outbreaks are often only identified after they reach high levels. A wide range of data is collected within healthcare settings; however, the extent to which this information is used to understand HCAI dynamics has not been quantified.

Aim

To examine the use of spatiotemporal analyses to identify and prevent HCAI transmission in healthcare settings, and to provide recommendations for expanding the use of these techniques.

Methods

A systematic review of the literature was undertaken, focusing on spatiotemporal examination of infectious diseases in healthcare settings. Abstracts and full-text articles were reviewed independently by two authors to determine inclusion.

Findings

In total, 146 studies met the inclusion criteria. There was considerable variation in the use of data, with surprisingly few studies (N = 22) using spatiotemporal-specific analyses to extend knowledge of HCAI transmission dynamics. The remaining 124 studies were descriptive. A modest increase in the application of statistical analyses has occurred in recent years.

Conclusion

The incorporation of spatiotemporal analysis has been limited in healthcare settings, with only 15% of studies including any such analysis. Analytical studies provided greater data on transmission dynamics and effective control interventions than studies without spatiotemporal analyses. This indicates the need for greater integration of spatiotemporal techniques into HCAI investigations, as even simple analyses provide significant improvements in the understanding of prevention over simple descriptive summaries.

Predominance of Klebsiella pneumoniae ST14 carrying CTX-M-15 causing neonatal sepsis in Tanzania

Background

Klebsiella pneumoniae strains expressing ESBLs are a predominant cause of hospital acquired infections. Here we describe the molecular epidemiology of these isolates in a tertiary hospital in Tanzania, as potential pathogens for neonatal infections.

Methods

Between April 2009 and March 2010 all Klebsiella pneumoniae isolates with phenotypic expression Extended Spectrum Beta Lactamase (ESBL) were collected and characterized. Identification was done using in house biochemical tests in case of ambiguous results confirmation was done using API 20E. Susceptibility testing was determined using the disc diffusion method followed by specific PCR and sequencing to determine ESBL genes. Phylogenetic analysis, Pulse field gel electrophoresis (PFGE) and Multi-Locus sequence typing (MLST) to PFGE clusters representative isolates were performed to determine clones of the isolates. Conjugation and hybridization were performed to determine the location of blaCTX-M-15 gene.

Results

A total of 92 non- repetitive ESBL producing K. pneumoniae representing 50.3% of Klebsiella pneumoniae isolates were characterized. These isolates were from blood 61 (66%), wound swab 13 (14%), urine 12 (13%) and pus 6 (7%) were analyzed. Most blood culture strains originated from neonatal unit 39/61(64%) and 22 (36%) of the blood culture isolates were from neonatal ICU. All isolates were resistant to gentamicin and 54% were resistant to ciprofloxacin. Using a similarity index of 80%, the isolates were assigned to thirteen clusters based on PFGE patterns and contained sub-clusters with identical strains indicating clonal outbreaks. Cluster X5, X7 and X8, and X9 were grouped into ST48, ST14 and ST348 respectively. Based on gyrA PCR- RFLP phylogenetic analysis all isolates were grouped as KpI. The predominant ESBL allele detected was bla_CTX-M-15 which was found in 76% of isolates, followed by bla_TEM-104 (19%), bla_SHV-11 (3.2%) and bla_TEM-176 (2%). The bla_CTX-M-15 gene was located in multiple conjugative IncF plasmids ranging from 25 kb-485 kb in size.

Conclusion

The high prevalence of bla_CTX-M-15 observed among ESBL producing K. pneumoniae in Tanzania, is possibly due to the spread of a common IncFII 145 kb plasmid and of certain clones such as ST14 and ST48. Furthermore the 485 kb plasmid detected is the largest plasmid reported to carry bla_CTX-M-15 todate.

Outbreak of pan-susceptible Klebsiella pneumoniae in a neonatal intensive care unit

We describe the outbreak of a pan-susceptible Klebsiella pneumoniae strain in a neonatal intensive care unit. A total of 7 neonates developed bacteraemia (37% attack rate), of whom 3 died (43% case fatality rate). A birth weight < 1500 g was the only statistically significant risk factor. Despite an extensive environmental investigation, the source was not identified.