# Genome-Based Characterization of Listeria monocytogenes, Costa Rica

María Giralt-Zúñiga, Mauricio Redondo-Solano, Alexandra Moura, Nathalie Tessaud-Rita, Hélène Bracq-Dieye, Guillaume Vales, Pierre Thouvenot, Alexandre Leclercq, Carolina Chaves-Ulate, Kattia Núñez-Montero, et al.

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To cite this version:

María Giralt-Zúñiga, Mauricio Redondo-Solano, Alexandra Moura, Nathalie Tessaud-Rita, Hélène Bracq-Dieye, et al. Genome-Based Characterization of Listeria monocytogenes, Costa Rica. Emerging Infectious Diseases, 2023, 29 (12), pp.2566-2569. 10.3201/eid2912.230774. pasteur-04323178

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# Genome-Based Characterization of *Listeria monocytogenes*, Costa Rica

María Giralt-Zúñiga,<fnref n="1" />,<fnref n="2" /> Mauricio Redondo-Solano,<fnref n="1" />
Alexandra Moura,<fnref n="1" /> Nathalie Tessaud-Rita,
Hélène Bracq-Dieye, Guillaume Vales,
Pierre Thouvenot, Alexandre Leclercq,
Carolina Chaves-Ulate, Kattia Núñez-Montero,<fnref n="3" />
Rossy Guillén-Watson, Olga Rivas-Solano,
Grettel Chanto-Chacón, Francisco Duarte-Martínez,
Vanessa Soto-Blanco, Javier Pizarro-Cerdá,
Marc Lecuit

DOI: https://doi.org/10.3201/eid2912.230774

Author affiliations: Institut Pasteur, Université Paris Cité, Inserm U1117, Biology of Infection Unit, National Reference Center, and WHO Collaborating Center *Listeria*, Paris, France (M. Giralt-Zúñiga, M. Redondo-Solano, A. Moura, N. Tessaud-Rita, H. Bracq-Dieye, G. Vales, P. Thouvenot, A. Leclercq, J. Pizarro-Cerdá, M. Lecuit); Instituto Tecnológico de Costa Rica, Cartago, Costa Rica (M. Giralt-Zúñiga, K. Núñez-Montero, R. Guillén-Watson, O. Rivas-Solano); University of Costa Rica, San José, Costa Rica (M. Redondo-Solano, C. Chaves-Ulate); Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Rios, Costa Rica (G. Chanto-Chacón, F. Duarte-Martínez); National Animal Health Service, Heredia, Costa Rica (V. Soto-Blanco); Necker Enfants Malades University Hospital, APHP, Institut Imlagine, Paris (M. Lecuit)

Genomic data on the foodborne pathogen *Listeria monocytogenes* from Central America are scarce. We analyzed 92 isolates collected during 2009–2019 from different regions in Costa Rica, compared those to publicly available genomes, and identified unrecognized outbreaks. Our findings suggest mandatory reporting of listeriosis in Costa Rica would improve pathogen surveillance.

*Listeria monocytogenes* is a gram-positive pathogen responsible for listeriosis, a severe foodborne infection that causes high hospitalization and mortality rates in at-risk populations, including older adults, immunocompromised persons, pregnant women, and newborns (1). *L. monocytogenes* diversity can be classified into lineages, genoserogroups, clonal complexes (CCs), and sequence types (STs), defined by multilocus sequence typing (MLST) (2).

Core-genome MLST (cgMLST) further identifies sublineages (SLs) and cgMLST types (CTs) (2). Major CCs and SLs are distributed globally and can be heterogeneous in terms of virulence; isolates from serogroup IVb (lineage I) often cause the most severe infections (2–4).

Pathogen surveillance using whole-genome sequencing (WGS) provides unprecedented resolution for identifying case clusters and contamination sources and for predicting strain virulence and antimicrobial resistance, which can aid in risk assessment (2,5). Previous studies confirmed *L. monocytogenes* in various foods in Costa Rica; reported contamination levels were 5%–20% in processed meat products and fresh cheeses (6,7). Because listeriosis is not a notifiable disease in Costa Rica, its prevalence is unknown, and diversity of *L. monocytogenes* circulating in the country is unclear.

To clarify the diversity of and potential public health risk from circulating strains, we used WGS to characterize 92 isolates recovered during 2009–2019 from 16 clinical, 67 food, and 9 production environment samples in Costa Rica (Appendix, https://wwwnc.cdc.gov/EID/article/29/12/23-0774-App1.pdf). When location data were available, isolates were from urban areas, including the capital city San José, and from rural areas where fresh cheese production is prevalent, including Alajuela, Naranjo, San Ramón, Vara Blanca, Upala, and Turrialba. Turrialba region accounts for 70% of fresh cheese produced in Costa Rica (Figure; Appendix).

We found that isolates from lineage I (95%, n = 88) and lineage II (5%, n = 4) were unevenly distributed into 12 different SLs and CCs (Figure; Appendix Figure 1). Those isolates included a new lineage I sublineage, designated SL1079 (new MLST singleton ST1079), which was identified in an isolate from shrimp (cgMLST type L1-SL1079-ST1079-CT1669). That isolate had an atypical genoserogroup IIb profile, designated IIb-v1, that differed from the classic IIb profile by the presence of *lmo0737*. WGS confirmed the presence of *lmo0737* and flanking genes *lmo0733*–39, typically found in lineage II isolates from serogroups IIa and IIc but only occasionally found in lineage I serogroup IVb-v1 (8). Of note, 80% of isolates investigated from both clinical and food-associated sources were from sublineages SL2/CC2 (66%, n = 61) and SL3/CC3 (14%, n = 13). SL2/CC2 (serogroup IVb) and SL3/CC3 (serogroup IIb) isolates are found worldwide and are associated with invasive infections (2–4). However, they are rarely the most prevalent genotypes (2,3). Available data from other countries in Central America confirmed

<footnote n="1">¹These first authors contributed equally to this article.</footnote>

<footnote n="2">²Current affiliation: Humboldt-Universität zu Berlin, Berlin, Germany.</footnote>

<footnote n="3">³Current affiliation: Universidad Autónoma de Chile, Temuco, Chile.</footnote>
<figure><img src="image_3.png" /><figcaption>**Figure.** Single linkage dendrogram of 92 isolates generated for genome-based characterization of *Listeria monocytogenes*, Costa Rica. Dendrogram is based on core-genome multilocus sequence typing; (cgMLST) allelic profiles (1,748-locus scheme). Branches are colored according to lineages: L1, red; L2, blue. Branches are labeled according to lineages, sublineages, and clonal complexes. Information on isolates' serogroup, and resistance profiles are provided in the columns. Colors in location column correspond to dots on map. Gray bars indicate clusters of isolates with ≤7 allelic differences out of 1,748 cgMLST loci. Presence of selected virulence and resistance genetic traits in each isolate is represented by dark blue boxes and empty boxes denote genes with premature stop codons. More details are provided in Appendix Figure 1 (https://wwwnc.cdc.gov/EID/article/29/12/23-0774-App1.pdf). CC, clonal complex; L, lineage; LIPI, listeria pathogenicity island; SL, sublineage.</figcaption></figure>
<table><caption>**Table.** Sequence types identified in a genome-based characterization of *Listeria monocytogenes*, Costa Rica*</caption><thead><tr><th rowspan="2">cgMLST type</th><th rowspan="2">CC</th><th rowspan="2">Serogroup</th><th colspan="3">No. isolates (%)</th><th rowspan="2">Food type</th><th rowspan="2">Isolation years</th><th rowspan="2">Genetic resistance traits</th></tr><tr><th>Total, n = 92</th><th>Clinical, n = 16</th><th>Nonclinical, n = 76</th></tr></thead><tbody><tr><td>L1-SL2-ST2-CT2715</td><td>CC2</td><td>IVb</td><td>8 (9)</td><td>4 (25)</td><td>4 (5)</td><td>Dairy, meat</td><td>2009, 2011, 2013, 2016–2017</td><td>bcrABC, qacA, LGI-2</td></tr><tr><td>L1-SL2-ST2-CT6120</td><td>CC2</td><td>IVb</td><td>10 (11)</td><td>2 (13)</td><td>8 (9)</td><td>Dairy</td><td>2010, 2013, 2016, 2018–2019</td><td>qacA, LGI-2</td></tr><tr><td>L1-SL2-ST2-CT2718</td><td>CC2</td><td>IVb</td><td>5 (5)</td><td>1 (6)</td><td>4 (5)</td><td>Dairy</td><td>2016, 2019</td><td>qacA</td></tr><tr><td>L1-SL2-ST1251-CT2780</td><td>CC2</td><td>IVb</td><td>3 (3)</td><td>1 (6)</td><td>2 (3)</td><td>Meat</td><td>2015–2016, 2018</td><td>qacA</td></tr><tr><td>L1-SL3-ST3-CT2730</td><td>CC3</td><td>IIb</td><td>9 (10)</td><td>0</td><td>9 (10)</td><td>Fish, meat</td><td>2016</td><td>bcrABC, SSI-1</td></tr><tr><td>L1-SL2-ST2-CT6072</td><td>CC2</td><td>IVb</td><td>5 (5)</td><td>0</td><td>5 (7)</td><td>Dairy</td><td>2019</td><td>LGI-2</td></tr><tr><td>L1-SL2-ST1627-CT6041</td><td>CC2</td><td>IVb</td><td>5 (5)</td><td>0</td><td>5 (7)</td><td>Dairy</td><td>2018–2019</td><td>LGI-2</td></tr><tr><td>L1-SL87-ST847-CT65</td><td>CC87</td><td>IIb</td><td>2 (2)</td><td>0</td><td>2 (3)</td><td>Meat</td><td>2016, 2019</td><td>NA</td></tr><tr><td>L1-SL3-ST1262/ST2762-CT2781</td><td>CC3</td><td>IIb</td><td>2 (2)</td><td>0</td><td>2 (3)</td><td>Dairy</td><td>2013</td><td>SSI-1</td></tr><tr><td>L1-SL5-ST5-CT2793</td><td>CC5</td><td>IIb</td><td>2 (2)</td><td>0</td><td>2 (3)</td><td>Fish, meat</td><td>2016</td><td>bcrABC, SSI-1</td></tr><tr><td>L1-SL2-ST2-CT2762</td><td>CC2</td><td>IVb</td><td>2 (2)</td><td>0</td><td>2 (3)</td><td>Mushrooms</td><td>2011</td><td>LGI-2</td></tr></tbody></table>

overrepresentation of SL2/CC2 and SL3/CC3 in Costa Rica (Appendix), which could be related to country's geographic location, climatic peculiarities, commercial trends, or natural reservoirs.

At the strain level, we identified 48 CTs, of which 44 (92%) were not previously reported. Eleven (23%) CTs included multiple isolates at a cutoff of 7 allelic differences of 1,748 cgMLST loci (2) (Table; Figure; Appendix Figures 1–3). Eight isolates were cgMLST type L1-SL2-ST2-CT2715, which accounted for 25% of clinical cases and spanned 9 years (Table).

Most human cases were associated with dairy products (Table). However, tracing to confirm the source of infection was not possible because most production is conducted by local farmers, often without traceability or attribution to the site of production.

Fresh cheese production is an economic staple in Costa Rica, and previous studies have reported *L. monocytogenes* detection in those products (7). Results from this study also show detection of identical strains of cgMLST type L1-SL2-ST2-CT6072 along the same production line, from raw materials to the final product, suggesting inadequate sanitation contributes to contamination (9).

*L. monocytogenes* is problematic for the food industry because it can survive and multiply under adverse environmental conditions (10). In this study, 90% of isolates carried ≥1 genetic element encoding for tolerance to disinfectants or stress. Markers of tolerance to disinfectants included *qacA* (51%, n = 47), *bcrABC* (23%, n = 21), and *emrC* (1%, n = 1). In addition, isolates had stress survival islet (SSI) genes, including SSI-1, conveying tolerance to low pH and high salt concentrations (21%, n = 19), and SSI-2 conveying, tolerance to high pH and oxidative stress (1%, n = 1), as well as *Listeria* genomic island (LGI) genes, including LGI-2 (50%, n = 48) and LGI-3 (1%, n = 1) conveying tolerance to metals. Those tolerances can make *L. monocytogenes* elimination from production sites more difficult.

This study provides insight into the diversity of *L. monocytogenes* strains circulating in Central America and can aid national reference institutions in promoting regulatory changes to guarantee mandatory listeriosis reporting. In addition, institutions should establish mechanisms to provide low-cost microbiologic analysis. We also recommend regular sampling of risk products and training of artisanal processors.

In conclusion, strengthened WGS surveillance in Costa Rica could assist in controlling *L. monocytogenes* and provide food producers with information on strain diversity and effective means of eradication. WGS surveillance also would enable authorities to detect outbreaks and trace sources of contamination.

This article was preprinted at https://doi.org/10.1101/2023.06.23.543262.

## Acknowledgments

We thank the submitters for depositing their data in public databases and Institut Pasteur teams for the curation and maintenance of Bacterial Isolate Genome Sequence Databases (BIGSdb) at Institut Pasteur, Paris, France (https://bigsdb.pasteur.fr). We also thank the CONAGEBIO from the Costa Rican Ministry of Environment and Energy (MINAE) for providing the permits to the access to biological material presented here (file no. CM-ITCR-003-2021).

<footnote>*Table includes types detected in this study comprising ≥2 isolates with a cutoff of 7 allelic differences, n = 11/48. CC, clonal complex; cgMLST, core-genome multilocus sequence typing; LGI, *Listeria* genomic island; NA, not applicable; SSI, stress survival islet.</footnote>
This work includes multilocus sequence typing
profiles publicly available on BIGSdb-Listeria
(https://bigsdb.pasteur.fr/listeria).

This work was developed within the framework of
agreements between Institut Pasteur and the University of
Costa Rica, and between Institut Pasteur and Instituto
Tecnológico de Costa Rica (amendment no.1 to the memo-
randum of understanding dated February 21, 2018), and
supported by Institut Pasteur, Inserm, Santé Publique
France, the government of France Investissement d'Avenir
program Laboratoire d'Excellence Integrative Biology
of Emerging Infectious Diseases (no. ANR-10-LABX-
62-IBEID), the Vice Rectory of Research of the Instituto
Tecnológico de Costa Rica (research project no. 1510160),
and the Vice Rectory of Research at the University of
Costa Rica (project nos. B2104 and B9026). Travel funds
for M.G.Z. were provided by the Instituto Tecnológico de
Costa Rica and the Consejo Nacional para Investigaciones
Científicas y Tecnológicas (CONICIT). Travel funds for
M.R.S. were provided by the Institut Français.

About the Author

Ms. Giralt-Zúñiga is currently a PhD student at the Molecular Microbiology Department of the Institute for Biology, Humboldt-Universität zu Berlin, Germany. Her research interests focus on infectious diseases and enteric pathogens.

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Address for correspondence. Marc Lecuit or Javier Pizarro-Cerda, 28 Rue du Docteur Roux, 75724 Paris CEDEX 15, France; email: marc.lecuit@pasteur.fr or javier.pizarro-cerda@pasteur.fr

Human *Taenia martis*
Neurocysticercosis,
Switzerland

Valentin K. Steinsiepe, Marie-Therese Ruf, Marco Rossi, Claudia Fricker-Feer, Danijela Kolenc, Brigitte Suter Buser, Maura Concu, Andreas Neumayr, Ulf C. Schneider

Author affiliations: Cantonal Hospital of Lucerne, Lucerne, Switzerland (V.K. Steinsiepe, M. Rossi, C. Fricker-Feer, D. Kolenc, U.C. Schneider); Swiss Tropical and Public Health Institute, Allschwil, Switzerland (M.-T. Ruf, M. Concu, A. Neumayr); University of Basel, Basel, Switzerland (M.-T. Ruf, M. Concu, A. Neumayr)

DOI: https://doi.org/10.3201/eid2912.230697

Neurocysticercosis is almost exclusively caused by *Taenia solium* tapeworms. We describe a case of neurocysticercosis in Switzerland caused by infection with *Taenia martis*, the marten tapeworm, and review all 5 published cases of human infection with the marten tapeworm. In epidemiologically nonplausible cases of neurocysticercosis, zoonotic spillover infections should be suspected.
# Genome-Based Characterization of *Listeria monocytogenes*, Costa Rica

## Appendix

## Materials and Methods

### Bacterial Isolation

The study included 92 *L. monocytogenes* isolates previously collected from different regions throughout Costa Rica (Figure in main manuscript; Appendix Table 1) and spanning eleven years (2009–2019). Clinical isolates (n = 16) were obtained by the Institute for Research and Teaching in Nutrition and Health (INCIENSA) in the context of the activities of the Costa Rican National Clinical Laboratory Network, comprised by laboratories of major hospitals, clinical settings, and the University of Costa Rica (UCR). Even though *L. monocytogenes* is not a notifiable disease in the country, there is an established criterium where bacterial pathogens that cause meningitis are sent to INCIENSA for confirmation of identification as well as antibiotic susceptibility tests. Isolates from food and food-production environments (n = 76) were obtained by the National Laboratory of Veterinary Services (LANASEVE) of National Animal Health Service (SENASA), which performs microbiology analysis for the surveillance of food safety in products of animal origin for human consumption, by the INCIENSA that also monitors the microbiological quality of food for human consumption, and by the UCR and the Instituto Tecnológico de Costa Rica (ITCR) in the scope of research projects and/or routine analyses for customers, as well as in the framework of a specific study to investigate *Listeria* spp. strains previously isolated by private entities regulated and accredited by the international standard INTE/ISO/IEC 17025:2017 for microbiological analysis that guarantee the results of their sampling process.
Bacterial isolation was performed as described previously, following either the Bacteriological Analytical Manual method for *Listeria* isolation (1), for isolates obtained by the UCR, ITCR and SENASA, or the ISO 11290-1:2017 method (2), for isolates obtained by the INCIENSA.

Isolate identification was performed by proteomic analysis by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, using the MicroFlex LT system with MBT library DB-5989 (Bruker Daltonics, Bremen, Germany), as previously described (3).

## DNA Extraction and Genome Sequencing

Isolates were cultured in Brain Heart Infusion Broth (BHI, Oxoid, Basingstoke UK) at 35°C overnight before use. DNA extraction was performed with the DNeasy Blood & Tissue Kit (QIAGEN, København Ø, Denmark-confirm), according to the instructions provided by the manufacturer. Qubit fluorometer (Thermo FisherScientific, Waltham, MA, USA) was used to evaluate DNA quantity and purity. Library preparation was performed with the Nextera XT DNA Sample Kit (Illumina, San Diego, CA, USA), and DNA sequencing was carried out on a NextSeq 500 platform (Illumina) using 2x 150-bp paired-end runs. Reads were trimmed using fqCleanER v.21.10 (https://gitlab.pasteur.fr/GIPhy/fqCleanER), and assemblies were obtained using SPAdes v.3.14.0 (4) and polished with Pilon v.1.23 (5).

## In Silico Molecular Typing

PCR-serogroups (6), multilocus sequence types (MLST) (7), core genome MLST (cgMLST) (8), and virulence and resistance profiles (8–14) were extracted from draft assemblies using BIGSdb-*Lm* (8,15) and BLASTN algorithm, as described before (8).

Minimum spanning trees were obtained from MLST and cgMLST profiles using BioNumerics v.7.6 (Applied-Maths, Sint-Martens-Latem, Belgium). MLST analyses also included 351 publicly available *L. monocytogenes* profiles from neighboring countries, obtained from BIGSdb-*Lm* (http://bigsdb.pasteur.fr/listeria; accessed on 16 February 2023). cgMLST-based dendrograms were built in BioNumerics v.7.6.3 (Applied Maths, Sint-Martens-Latem, Belgium) using categorical differences and the single-linkage clustering method, and visualized with iTOL v.5 (16).
**Data Availability**

Sequence data was made publicly available in NCBI/EBI/DDJJ databases (BioProject no. PRJEB20026).

**Supplementary References**

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14. Harter E, Wagner EM, Zaiser A, Halecker S, Wagner M, Rychli K. Stress survival islet 2, predominantly present in *Listeria monocytogenes* strains of sequence type 121, is involved in the alkaline and oxidative stress responses. Appl Environ Microbiol. 2017;83:e00827-17. PubMed https://doi.org/10.1128/AEM.00827-17

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<table><caption>Appendix Table 1. Isolate metadata and genome metrics of *Listeria monocytogenes* sequenced in this study (n = 92).</caption><thead><tr><th>Isolate no.</th><th>No. bases after filtering</th><th>Coverage</th><th>No. contigs</th><th>Total length, bp</th><th>N50, bp</th><th>% GC</th><th>% cgMLST loci tagged</th><th>Source type</th><th>Sample type</th><th>Geographic location</th><th>Isolation year</th><th>Serogroup</th><th>Lineage</th><th>Clonal complex, MLST</th><th>Sublineage, cgMLST</th><th>cgMLST type</th><th>BIGSdb ID</th></tr></thead><tbody><tr><td>CLIP 2017/00419</td><td>2.40E+08</td><td>83</td><td>38</td><td>3.01E+06</td><td>1.94E+05</td><td>37.8</td><td>99.7</td><td>F</td><td>Sausage</td><td>San José</td><td>2016</td><td>IVb</td><td>I</td><td>CC1</td><td>SL1</td><td>CT2786</td><td>ID102753</td></tr><tr><td>CLIP 2019/02752</td><td>3.82E+08</td><td>132</td><td>30</td><td>2.99E+06</td><td>2.62E+05</td><td>37.82</td><td>99.8</td><td>F</td><td>Cheese</td><td>Vara Blanca</td><td>2019</td><td>IVb</td><td>I</td><td>CC1</td><td>SL1</td><td>CT333</td><td>ID102785</td></tr><tr><td>CLIP 2019/02623</td><td>4.20E+08</td><td>145</td><td>43</td><td>3.04E+06</td><td>1.92E+05</td><td>37.8</td><td>99.9</td><td>H</td><td>CSF</td><td>San José</td><td>2018</td><td>IVb</td><td>I</td><td>CC1</td><td>SL1</td><td>CT333</td><td>ID102774</td></tr><tr><td>CLIP 2019/02615</td><td>5.11E+08</td><td>176</td><td>38</td><td>3.02E+06</td><td>2.55E+05</td><td>37.81</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC1</td><td>SL1</td><td>CT6042</td><td>ID102766</td></tr><tr><td>CLIP 2017/00404</td><td>3.05E+08</td><td>105</td><td>58</td><td>3.06E+06</td><td>1.43E+05</td><td>37.82</td><td>99.9</td><td>F</td><td>Cheese</td><td>ND</td><td>2011</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102739</td></tr><tr><td>CLIP 2017/00409</td><td>2.52E+08</td><td>87</td><td>110</td><td>3.05E+06</td><td>7.45E+04</td><td>37.85</td><td>99.3</td><td>F</td><td>Cheese</td><td>Cartago</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102744</td></tr><tr><td>CLIP 2017/00417</td><td>5.93E+08</td><td>205</td><td>49</td><td>3.01E+06</td><td>1.39E+05</td><td>37.88</td><td>99.8</td><td>F</td><td>Sausage</td><td>San José</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102751</td></tr><tr><td>CLIP 2019/02742</td><td>5.20E+08</td><td>179</td><td>47</td><td>3.17E+06</td><td>1.98E+05</td><td>37.7</td><td>99.8</td><td>F</td><td>Cheese</td><td>Upala</td><td>2017</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102775</td></tr><tr><td>CLIP 2017/00398</td><td>4.34E+08</td><td>150</td><td>58</td><td>3.17E+06</td><td>1.50E+05</td><td>37.69</td><td>99.8</td><td>H</td><td>Blood</td><td>Guanacaste†</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102733</td></tr><tr><td>CLIP 2017/00399</td><td>4.18E+08</td><td>144</td><td>51</td><td>3.16E+06</td><td>1.32E+05</td><td>37.69</td><td>99.8</td><td>H</td><td>Blood</td><td>Limón†</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102734</td></tr><tr><td>CLIP 2017/00400</td><td>3.59E+08</td><td>124</td><td>40</td><td>3.10E+06</td><td>2.23E+05</td><td>37.75</td><td>99.8</td><td>H</td><td>Blood</td><td>Limón†</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102735</td></tr><tr><td>CLIP 2017/00403</td><td>5.40E+08</td><td>186</td><td>52</td><td>3.17E+06</td><td>1.39E+05</td><td>37.69</td><td>99.8</td><td>H</td><td>CSF</td><td>Heredia†</td><td>2009</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2715</td><td>ID102738</td></tr><tr><td>CLIP 2017/00391</td><td>4.72E+08</td><td>163</td><td>51</td><td>3.04E+06</td><td>1.61E+05</td><td>37.84</td><td>99.9</td><td>H</td><td>Blood</td><td>Cartago†</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2716</td><td>ID102726</td></tr><tr><td>CLIP 2017/00405</td><td>4.46E+08</td><td>154</td><td>38</td><td>3.05E+06</td><td>1.39E+05</td><td>37.83</td><td>99.9</td><td>H</td><td>Blood</td><td>Limón†</td><td>2010</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2717</td><td>ID102740</td></tr><tr><td>CLIP 2019/02751</td><td>4.38E+08</td><td>151</td><td>34</td><td>3.06E+06</td><td>2.73E+05</td><td>37.84</td><td>99.9</td><td>F</td><td>Cheese</td><td>Vara Blanca</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2718</td><td>ID102784</td></tr><tr><td>CLIP 2019/02753</td><td>3.36E+08</td><td>116</td><td>29</td><td>3.06E+06</td><td>2.72E+05</td><td>37.84</td><td>99.9</td><td>F</td><td>Cheese</td><td>San Ramón</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2718</td><td>ID102786</td></tr><tr><td>CLIP 2019/02754</td><td>3.03E+08</td><td>105</td><td>26</td><td>2.97E+06</td><td>3.33E+05</td><td>37.9</td><td>99.9</td><td>F</td><td>Cheese</td><td>San Ramón</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2718</td><td>ID102787</td></tr><tr><td>CLIP 2019/02756</td><td>2.54E+08</td><td>87</td><td>58</td><td>3.01E+06</td><td>1.44E+05</td><td>37.88</td><td>99.8</td><td>F</td><td>Cheese</td><td>Zarcero</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2718</td><td>ID102789</td></tr><tr><td>CLIP 2017/00396</td><td>5.98E+08</td><td>206</td><td>51</td><td>3.01E+06</td><td>1.41E+05</td><td>37.88</td><td>99.9</td><td>H</td><td>CSF</td><td>San José</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2718</td><td>ID102731</td></tr><tr><td>CLIP 2017/00407</td><td>4.45E+08</td><td>153</td><td>58</td><td>3.06E+06</td><td>1.52E+05</td><td>37.83</td><td>99.9</td><td>H</td><td>CSF</td><td>Cartago†</td><td>2010</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2719</td><td>ID102742</td></tr><tr><td>CLIP 2017/00390</td><td>4.06E+08</td><td>140</td><td>42</td><td>3.04E+06</td><td>2.02E+05</td><td>37.81</td><td>99.9</td><td>H</td><td>CSF</td><td>Alajuela†</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2720</td><td>ID102725</td></tr><tr><td>CLIP 2017/00392</td><td>5.23E+08</td><td>180</td><td>59</td><td>3.03E+06</td><td>1.52E+05</td><td>37.81</td><td>99.8</td><td>H</td><td>Blood</td><td>Alajuela†</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2721</td><td>ID102727</td></tr><tr><td>CLIP 2017/00401</td><td>3.46E+08</td><td>119</td><td>38</td><td>2.96E+06</td><td>1.50E+05</td><td>37.85</td><td>99.8</td><td>F</td><td>Mushroom</td><td>ND</td><td>2011</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2762</td><td>ID102736</td></tr><tr><td>CLIP 2017/00402</td><td>2.98E+08</td><td>103</td><td>42</td><td>2.99E+06</td><td>1.38E+05</td><td>37.81</td><td>99.8</td><td>F</td><td>Mushroom</td><td>ND</td><td>2011</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2762</td><td>ID102737</td></tr><tr><td>CLIP 2017/00426</td><td>2.63E+08</td><td>91</td><td>55</td><td>3.04E+06</td><td>1.87E+05</td><td>37.84</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José†</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2779</td><td>ID102760</td></tr><tr><td>CLIP 2017/00420</td><td>1.59E+08</td><td>55</td><td>87</td><td>3.05E+06</td><td>9.85E+04</td><td>37.83</td><td>99.9</td><td>F</td><td>Sausage</td><td>San José</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2780</td><td>ID102754</td></tr><tr><td>CLIP 2017/00421</td><td>2.61E+08</td><td>90</td><td>59</td><td>3.05E+06</td><td>1.53E+05</td><td>37.83</td><td>100</td><td>F</td><td>Sausage</td><td>San José</td><td>2015</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2780</td><td>ID102755</td></tr><tr><td>CLIP 2019/02622</td><td>3.75E+08</td><td>129</td><td>48</td><td>3.01E+06</td><td>2.38E+05</td><td>37.86</td><td>99.9</td><td>H</td><td>Blood</td><td>San José</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2780</td><td>ID102773</td></tr><tr><td>CLIP 2017/00413</td><td>5.63E+08</td><td>194</td><td>61</td><td>3.08E+06</td><td>1.29E+05</td><td>37.79</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José†</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT2787</td><td>ID102747</td></tr><tr><td>CLIP 2019/02613</td><td>4.08E+08</td><td>141</td><td>41</td><td>3.00E+06</td><td>1.73E+05</td><td>37.86</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6040</td><td>ID102764</td></tr><tr><td>CLIP 2019/02610</td><td>4.27E+08</td><td>147</td><td>67</td><td>3.05E+06</td><td>1.45E+05</td><td>37.79</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6041</td><td>ID102761</td></tr><tr><td>CLIP 2019/02612</td><td>3.79E+08</td><td>131</td><td>62</td><td>3.11E+06</td><td>1.61E+05</td><td>37.86</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6041</td><td>ID102763</td></tr><tr><td>CLIP 2019/02616</td><td>3.38E+08</td><td>117</td><td>65</td><td>3.05E+06</td><td>1.11E+05</td><td>37.79</td><td>99.8</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6041</td><td>ID102767</td></tr><tr><td>CLIP 2019/02618</td><td>3.65E+08</td><td>126</td><td>82</td><td>3.05E+06</td><td>1.10E+05</td><td>37.79</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6041</td><td>ID102769</td></tr><tr><td>CLIP 2019/02750</td><td>4.94E+08</td><td>170</td><td>50</td><td>3.05E+06</td><td>1.98E+05</td><td>37.79</td><td>99.9</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6041</td><td>ID102783</td></tr><tr><td>CLIP 2019/02621</td><td>5.80E+08</td><td>200</td><td>51</td><td>3.08E+06</td><td>1.61E+05</td><td>37.84</td><td>99.9</td><td>H</td><td>Blood</td><td>San José</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6045</td><td>ID102772</td></tr><tr><td>CLIP 2019/02611</td><td>3.92E+08</td><td>135</td><td>76</td><td>3.09E+06</td><td>1.98E+05</td><td>37.8</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6046</td><td>ID102762</td></tr><tr><td>CLIP 2019/02617</td><td>3.55E+08</td><td>122</td><td>65</td><td>3.03E+06</td><td>1.26E+05</td><td>37.84</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6047</td><td>ID102768</td></tr><tr><td>CLIP 2019/02745</td><td>3.90E+08</td><td>135</td><td>35</td><td>2.97E+06</td><td>2.40E+05</td><td>37.91</td><td>99.9</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6063</td><td>ID102778</td></tr><tr><td>CLIP 2019/02748</td><td>4.82E+08</td><td>166</td><td>43</td><td>3.04E+06</td><td>2.71E+05</td><td>37.85</td><td>99.9</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6065</td><td>ID102781</td></tr><tr><td>CLIP 2019/02757</td><td>3.04E+08</td><td>105</td><td>68</td><td>3.10E+06</td><td>2.39E+05</td><td>37.79</td><td>99.7</td><td>F</td><td>Cheese</td><td>San Isidro</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6066</td><td>ID102790</td></tr><tr><td>CLIP 2019/02744</td><td>4.94E+08</td><td>170</td><td>51</td><td>3.04E+06</td><td>2.38E+05</td><td>37.85</td><td>99.8</td><td>F</td><td>Cheese</td><td>Capellades</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6067</td><td>ID102777</td></tr><tr><td>CLIP 2019/02749</td><td>4.85E+08</td><td>167</td><td>40</td><td>3.04E+06</td><td>1.59E+05</td><td>37.85</td><td>99.9</td><td>F</td><td>Cheese</td><td>Santa Cruz</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6069</td><td>ID102782</td></tr><tr><td>CLIP 2019/02747</td><td>4.08E+08</td><td>141</td><td>74</td><td>3.07E+06</td><td>1.98E+05</td><td>37.83</td><td>99.9</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6070</td><td>ID102780</td></tr><tr><td>CLIP 2019/02764</td><td>7.56E+08</td><td>261</td><td>84</td><td>3.16E+06</td><td>3.21E+05</td><td>37.76</td><td>99.8</td><td>F</td><td>Raw milk</td><td>Turrialba</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6072</td><td>ID102797</td></tr><tr><td>CLIP 2019/02765</td><td>7.81E+08</td><td>269</td><td>59</td><td>3.12E+06</td><td>2.06E+05</td><td>37.79</td><td>99.9</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6072</td><td>ID102798</td></tr></tbody></table>
<table><thead><tr><th>Isolate no.</th><th>No. bases after filtering</th><th>Coverage</th><th>No. contigs</th><th>Total length, bp</th><th>N50, bp</th><th>% GC</th><th>% cgMLST loci tagged</th><th>Source type</th><th>Sample type</th><th>Geographic location</th><th>Isolation year</th><th>Serogroup</th><th>Lineage</th><th>Clonal complex, MLST</th><th>Sublineage, cgMLST</th><th>cgMLST type</th><th>BIGSdb ID</th></tr></thead><tbody><tr><td>CLIP 2019/02759</td><td>1.24E+09</td><td>426</td><td>120</td><td>3.11E+06</td><td>3.60E+05</td><td>38</td><td>99.9</td><td>PE</td><td>Drain</td><td>Turrialba</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6072</td><td>ID102792</td></tr><tr><td>CLIP 2019/02760</td><td>7.47E+08</td><td>258</td><td>47</td><td>3.12E+06</td><td>3.60E+05</td><td>37.77</td><td>99.9</td><td>PE</td><td>Tank</td><td>Turrialba</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6072</td><td>ID102793</td></tr><tr><td>CLIP 2019/02761</td><td>7.06E+08</td><td>243</td><td>62</td><td>3.15E+06</td><td>3.63E+05</td><td>37.81</td><td>99.9</td><td>PE</td><td>Cooling chamber</td><td>Turrialba</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6072</td><td>ID102794</td></tr><tr><td>CLIP 2017/00372</td><td>1.76E+08</td><td>61</td><td>90</td><td>3.12E+06</td><td>9.53E+04</td><td>37.69</td><td>99.9</td><td>PE</td><td>Soil</td><td>Cartago†</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6116</td><td>ID102721</td></tr><tr><td>CLIP 2017/00424</td><td>5.53E+08</td><td>191</td><td>32</td><td>3.04E+06</td><td>1.98E+05</td><td>37.81</td><td>99.9</td><td>F</td><td>Cheese</td><td>Heredia</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6117</td><td>ID102758</td></tr><tr><td>CLIP 2019/02755</td><td>3.66E+08</td><td>126</td><td>37</td><td>3.04E+06</td><td>3.55E+05</td><td>37.84</td><td>99.9</td><td>F</td><td>Cheese</td><td>Zarcero</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6118</td><td>ID102788</td></tr><tr><td>CLIP 2017/00412</td><td>2.08E+08</td><td>72</td><td>60</td><td>3.06E+06</td><td>1.35E+05</td><td>37.8</td><td>99.8</td><td>F</td><td>Cheese</td><td>Cartago</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6119</td><td>ID102746</td></tr><tr><td>CLIP 2017/00411</td><td>2.77E+08</td><td>96</td><td>57</td><td>3.08E+06</td><td>2.81E+05</td><td>37.8</td><td>99.8</td><td>F</td><td>Cheese</td><td>Cartago</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102745</td></tr><tr><td>CLIP 2017/00415</td><td>2.78E+08</td><td>96</td><td>51</td><td>3.04E+06</td><td>1.55E+05</td><td>37.84</td><td>99.9</td><td>F</td><td>Cheese</td><td>Cartago†</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102749</td></tr><tr><td>CLIP 2017/00418</td><td>2.74E+08</td><td>94</td><td>48</td><td>3.04E+06</td><td>1.50E+05</td><td>37.84</td><td>99.9</td><td>F</td><td>Cheese</td><td>San José</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102752</td></tr><tr><td>CLIP 2017/00423</td><td>2.62E+08</td><td>90</td><td>63</td><td>3.08E+06</td><td>1.39E+05</td><td>37.8</td><td>99.9</td><td>F</td><td>Cheese</td><td>Cartago</td><td>2013</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102757</td></tr><tr><td>CLIP 2019/02614</td><td>2.43E+08</td><td>84</td><td>90</td><td>3.08E+06</td><td>9.05E+04</td><td>37.81</td><td>99.4</td><td>F</td><td>Cheese</td><td>San José</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102765</td></tr><tr><td>CLIP 2019/02746</td><td>3.45E+08</td><td>119</td><td>59</td><td>3.08E+06</td><td>1.61E+05</td><td>37.81</td><td>99.8</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2018</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102779</td></tr><tr><td>CLIP 2019/02762</td><td>6.86E+08</td><td>236</td><td>475</td><td>3.27E+06</td><td>2.73E+05</td><td>39.67</td><td>99.8</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102795</td></tr><tr><td>CLIP 2019/02763</td><td>9.18E+08</td><td>317</td><td>136</td><td>3.12E+06</td><td>3.58E+05</td><td>38.07</td><td>99.9</td><td>F</td><td>Raw milk</td><td>Turrialba</td><td>2019</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102796</td></tr><tr><td>CLIP 2017/00393</td><td>4.76E+08</td><td>164</td><td>59</td><td>3.08E+06</td><td>1.50E+05</td><td>37.8</td><td>99.9</td><td>H</td><td>Blood</td><td>Cartago†</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102728</td></tr><tr><td>CLIP 2017/00408</td><td>4.09E+08</td><td>141</td><td>66</td><td>3.08E+06</td><td>1.36E+05</td><td>37.81</td><td>99.9</td><td>H</td><td>CSF</td><td>Cartago†</td><td>2010</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6120</td><td>ID102743</td></tr><tr><td>CLIP 2017/00406</td><td>6.63E+08</td><td>228</td><td>60</td><td>3.07E+06</td><td>1.38E+05</td><td>37.79</td><td>99.9</td><td>H</td><td>CSF</td><td>Cartago†</td><td>2015</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6121</td><td>ID102741</td></tr><tr><td>CLIP 2017/00389</td><td>3.43E+08</td><td>118</td><td>41</td><td>3.05E+06</td><td>1.39E+05</td><td>37.83</td><td>99.9</td><td>F</td><td>Meat</td><td>ND</td><td>2016</td><td>IVb</td><td>I</td><td>CC2</td><td>SL2</td><td>CT6122</td><td>ID102724</td></tr><tr><td>CLIP 2019/02758</td><td>8.26E+08</td><td>285</td><td>31</td><td>2.91E+06</td><td>4.33E+05</td><td>37.91</td><td>99.8</td><td>F</td><td>Cheese</td><td>Naranjo</td><td>2019</td><td>IVb</td><td>I</td><td>CC217</td><td>SL217</td><td>CT222</td><td>ID102791</td></tr><tr><td>CLIP 2017/00395</td><td>3.03E+08</td><td>104</td><td>41</td><td>3.00E+06</td><td>1.95E+05</td><td>37.79</td><td>99.9</td><td>F</td><td>Sausage</td><td>ND</td><td>2016</td><td>IVb</td><td>I</td><td>CC6</td><td>SL6</td><td>CT2761</td><td>ID102730</td></tr><tr><td>CLIP 2017/00383</td><td>3.27E+08</td><td>113</td><td>59</td><td>3.03E+06</td><td>1.55E+05</td><td>37.82</td><td>99.9</td><td>F</td><td>Shrimp</td><td>San José†</td><td>2016</td><td>IIb-v1</td><td>I</td><td>ST1079</td><td>SL1079</td><td>CT1669</td><td>ID102722</td></tr><tr><td>CLIP 2017/00357</td><td>3.37E+08</td><td>116</td><td>53</td><td>3.14E+06</td><td>1.58E+05</td><td>37.75</td><td>99.8</td><td>F</td><td>Ground beef</td><td>San José†</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT1674</td><td>ID102707</td></tr><tr><td>CLIP 2017/00366</td><td>3.20E+08</td><td>110</td><td>51</td><td>3.10E+06</td><td>1.97E+05</td><td>37.79</td><td>99.9</td><td>PE</td><td>Drain</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT1674</td><td>ID102716</td></tr><tr><td>CLIP 2017/00358</td><td>2.38E+08</td><td>82</td><td>45</td><td>3.05E+06</td><td>1.34E+05</td><td>37.81</td><td>99.8</td><td>F</td><td>Chicken wings</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102708</td></tr><tr><td>CLIP 2017/00360</td><td>3.67E+08</td><td>127</td><td>43</td><td>3.05E+06</td><td>1.86E+05</td><td>37.81</td><td>99.8</td><td>F</td><td>Pork</td><td>Heredia</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102710</td></tr><tr><td>CLIP 2017/00361</td><td>5.29E+08</td><td>183</td><td>44</td><td>3.05E+06</td><td>1.87E+05</td><td>37.81</td><td>99.8</td><td>F</td><td>Pork</td><td>San José†</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102711</td></tr><tr><td>CLIP 2017/00363</td><td>4.02E+08</td><td>139</td><td>51</td><td>3.05E+06</td><td>1.42E+05</td><td>37.81</td><td>99.7</td><td>F</td><td>Cheese</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102713</td></tr><tr><td>CLIP 2017/00364</td><td>4.97E+08</td><td>171</td><td>44</td><td>3.05E+06</td><td>1.69E+05</td><td>37.81</td><td>99.7</td><td>F</td><td>Ground beef</td><td>San José†</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102714</td></tr><tr><td>CLIP 2017/00365</td><td>2.15E+08</td><td>74</td><td>43</td><td>3.05E+06</td><td>1.97E+05</td><td>37.81</td><td>99.8</td><td>F</td><td>Tilapia</td><td>Guanacaste†</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102715</td></tr><tr><td>CLIP 2017/00359</td><td>3.82E+08</td><td>132</td><td>40</td><td>3.05E+06</td><td>3.71E+05</td><td>37.81</td><td>99.8</td><td>PE</td><td>Drain</td><td>Alajuela</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102709</td></tr><tr><td>CLIP 2017/00370</td><td>3.05E+08</td><td>105</td><td>40</td><td>3.05E+06</td><td>1.97E+05</td><td>37.81</td><td>99.8</td><td>PE</td><td>Drain</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102719</td></tr><tr><td>CLIP 2017/00371</td><td>5.02E+08</td><td>173</td><td>42</td><td>3.05E+06</td><td>2.36E+05</td><td>37.81</td><td>99.7</td><td>PE</td><td>Drain</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2730</td><td>ID102720</td></tr><tr><td>CLIP 2017/00422</td><td>2.31E+08</td><td>80</td><td>39</td><td>3.04E+06</td><td>2.53E+05</td><td>37.92</td><td>99.7</td><td>F</td><td>Cheese</td><td>Cartago</td><td>2013</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2781</td><td>ID102756</td></tr><tr><td>CLIP 2017/00425</td><td>2.84E+08</td><td>98</td><td>39</td><td>3.04E+06</td><td>1.97E+05</td><td>37.93</td><td>99.7</td><td>F</td><td>Cheese</td><td>Cartago</td><td>2013</td><td>IIb</td><td>I</td><td>CC3</td><td>SL3</td><td>CT2781</td><td>ID102759</td></tr><tr><td>CLIP 2017/00367</td><td>2.62E+08</td><td>90</td><td>79</td><td>3.11E+06</td><td>2.36E+05</td><td>37.79</td><td>99.9</td><td>PE</td><td>Cooling chamber</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC5</td><td>SL5</td><td>CT2783</td><td>ID102717</td></tr><tr><td>CLIP 2017/00362</td><td>4.62E+08</td><td>159</td><td>74</td><td>3.11E+06</td><td>1.35E+05</td><td>37.77</td><td>99.9</td><td>F</td><td>Tilapia</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC5</td><td>SL5</td><td>CT2793</td><td>ID102712</td></tr><tr><td>CLIP 2017/00368</td><td>5.08E+08</td><td>175</td><td>59</td><td>3.10E+06</td><td>1.53E+05</td><td>37.79</td><td>99.9</td><td>F</td><td>Beef</td><td>Heredia†</td><td>2016</td><td>IIb</td><td>I</td><td>CC5</td><td>SL5</td><td>CT2793</td><td>ID102718</td></tr><tr><td>CLIP 2017/00414</td><td>2.13E+08</td><td>73</td><td>77</td><td>2.93E+06</td><td>1.20E+05</td><td>37.86</td><td>99.4</td><td>F</td><td>Cheese</td><td>Heredia†</td><td>2013</td><td>IIb</td><td>I</td><td>CC506</td><td>SL506</td><td>CT2776</td><td>ID102748</td></tr><tr><td>CLIP 2019/02619</td><td>3.78E+08</td><td>130</td><td>39</td><td>2.97E+06</td><td>3.04E+05</td><td>37.88</td><td>99.9</td><td>F</td><td>Chorizo</td><td>Heredia</td><td>2019</td><td>IIb</td><td>I</td><td>CC87</td><td>SL87</td><td>CT6044</td><td>ID102770</td></tr><tr><td>CLIP 2017/00416</td><td>2.36E+08</td><td>81</td><td>38</td><td>2.92E+06</td><td>1.99E+05</td><td>37.91</td><td>99.9</td><td>F</td><td>Sausage</td><td>San José</td><td>2016</td><td>IIb</td><td>I</td><td>CC87</td><td>SL87</td><td>CT65</td><td>ID102750</td></tr><tr><td>CLIP 2019/02620</td><td>3.96E+08</td><td>137</td><td>39</td><td>2.97E+06</td><td>2.09E+05</td><td>37.88</td><td>99.9</td><td>F</td><td>Chorizo</td><td>San José</td><td>2019</td><td>IIb</td><td>I</td><td>CC87</td><td>SL87</td><td>CT65</td><td>ID102771</td></tr><tr><td>CLIP 2017/00397</td><td>4.04E+08</td><td>139</td><td>28</td><td>3.09E+06</td><td>3.73E+05</td><td>37.87</td><td>100</td><td>F</td><td>Sausage</td><td>ND</td><td>2016</td><td>IIc</td><td>II</td><td>CC9</td><td>SL9</td><td>CT13239</td><td>ID102732</td></tr><tr><td>CLIP 2017/00388</td><td>2.98E+08</td><td>103</td><td>44</td><td>3.04E+06</td><td>2.02E+05</td><td>37.8</td><td>100</td><td>F</td><td>Pork</td><td>ND</td><td>2016</td><td>IIc</td><td>II</td><td>CC9</td><td>SL9</td><td>CT1668</td><td>ID102723</td></tr></tbody></table>
<table><thead><tr><th>Isolate no.</th><th>No. bases after filtering</th><th>Coverage</th><th>No. contigs</th><th>Total length, bp</th><th>N50, bp</th><th>% GC</th><th>% cgMLST loci tagged</th><th>Source type</th><th>Sample type</th><th>Geographic location</th><th>Isolation year</th><th>Serogroup</th><th>Lineage</th><th>Clonal complex, MLST</th><th>Sublineage, cgMLST</th><th>cgMLST type</th><th>BIGSdb ID</th></tr></thead><tbody><tr><td>CLIP 2017/00394</td><td>3.41E+08</td><td>117</td><td>38</td><td>3.09E+06</td><td>2.01E+05</td><td>37.79</td><td>100</td><td>F</td><td>Frozen vegetables</td><td>ND</td><td>2016</td><td>IIa</td><td>II</td><td>CC121</td><td>SL121</td><td>CT909</td><td>ID102729</td></tr><tr><td>CLIP 2019/02743</td><td>3.86E+08</td><td>133</td><td>18</td><td>2.83E+06</td><td>3.82E+05</td><td>37.93</td><td>99.9</td><td>F</td><td>Cheese</td><td>Turrialba</td><td>2018</td><td>IIa</td><td>II</td><td>CC19</td><td>SL378</td><td>CT6064</td><td>ID102776</td></tr></tbody></table>

<footnote>*BIGSdb, Bacterial Isolate Genome Sequence Database (17); cgMLST, core-genome multilocus sequence typing; F, food; H, human; ID, identification; MLST, multilocus sequence typing; ND, not done; PE, production environment.</footnote>

<footnote>†Geographic information available only at the level of the province.</footnote>
<table><caption>**Appendix Table 2.** Previously reported cgMLST types detected in this study (cutoff of 7 or less allelic differences out of 1748 cgMLST loci, Institut Pasteur scheme)</caption><thead><tr><th rowspan="2">cgMLST Type<br>(CC, serogroup)</th><th colspan="2">Source (item)</th><th rowspan="2">Studies from other<br>countries</th><th rowspan="2">Source lab</th><th rowspan="2">NCBI/EBI/DDJJ<br>accession no.</th><th rowspan="2">Reference<br>no.</th></tr><tr><th>This study</th><th>Other studies</th></tr></thead><tbody><tr><td>Lineage I<br>L1-SL217-ST217-<br>CT222 (CC217, IVb)</td><td>F (dairy)</td><td>H, F (salad)</td><td>US</td><td>CDC</td><td>SRR1021894,<br>SRR1027089</td><td>(8)</td></tr><tr><td>L1-SL1-ST1-CT333<br>(CC1, IVb)</td><td>H, F (dairy)</td><td>H</td><td>US</td><td>CDC</td><td>SRR1043171,<br>SRR7057542</td><td>(8,17)</td></tr><tr><td>L1-SL87-ST847-<br>CT65 (CC87, IIb)</td><td>F (meat)</td><td>F (avocado)</td><td>MX</td><td>FDA</td><td>SRR975360</td><td>(8)</td></tr><tr><td>Lineage II<br>L2-SL121-ST121-<br>CT909 (CC121, IIa)</td><td>F (frozen<br>vegetables)</td><td>H, F, PE, FE, A</td><td>CL, DK, FR, DE, LV,<br>NO, PL, NL, UK, US</td><td>KMAHVH,<br>ANSES,<br>ECDC, IP,<br>UWLMO,<br>UKHSA,<br>FDA, RKI</td><td>ERR1304231,<br>ERR1738638,<br>ERR1738650,<br>ERR2522041,<br>ERR2522263,<br>ERR2522276,<br>ERR2522284,<br>ERR2522292,<br>ERR2522294,<br>ERR2522295,<br>ERR2522297,<br>ERR2522312,<br>ERR2522337,<br>ERR2522338,<br>ERR2522353,<br>ERR2522363,<br>ERR2522371,<br>ERR2522810,<br>ERR3040059,<br>ERR3040061,<br>ERR3040067,<br>ERR3040072,<br>ERR3040073,<br>ERR3040075,<br>ERR3040076,<br>ERR3040078,<br>ERR3040083,<br>ERR3040104,<br>ERR4176463,<br>ERR4176497,<br>ERR4176536,<br>ERR4176606,<br>ERR4176666,<br>ERR4176794,<br>ERR4648214,<br>SRR10753542,<br>SRR10753574,<br>SRR10753599,<br>SRR10753600,<br>SRR10753602,<br>SRR11004717,<br>SRR13072765,<br>SRR14783257,<br>SRR15245555,<br>SRR15245949,<br>SRR20053048,<br>SRR2040689,<br>SRR4052010,<br>SRR4052014,<br>SRR4052068,<br>SRR4052071,<br>SRR4052072,<br>SRR4052073,<br>SRR4052161,<br>SRR4124934,<br>SRR4124940,<br>SRR5133499,<br>SRR5318940,</td><td>(8,10,18,19)</td></tr></tbody></table>
<table><thead><tr><th rowspan="2">cgMLST Type<br>(CC, serogroup)</th><th colspan="2">Source (item)</th><th rowspan="2">Studies from other<br>countries</th><th rowspan="2">Source lab</th><th rowspan="2">NCBI/EBI/DDJJ<br>accession no.</th><th rowspan="2">Reference<br>no.</th></tr><tr><th>This study</th><th>Other studies</th></tr></thead><tbody><tr><td></td><td></td><td></td><td></td><td></td><td>SRR5526029,<br>SRR5526031,<br>SRR5526035,<br>SRR5526085,<br>SRR5526092,<br>SRR5526094,<br>SRR5526097,<br>SRR5526099,<br>SRR5526101,<br>SRR5526105,<br>SRR5526120,<br>SRR5526126,<br>SRR5526128,<br>SRR5526130,<br>SRR5526135,<br>SRR5526137,<br>SRR5526138,<br>SRR5526142,<br>SRR5526145,<br>SRR5526155,<br>SRR5647016,<br>SRR5647027,<br>SRR5647029,<br>SRR5647030,<br>SRR6966182,<br>SRR7403111,<br>SRR7410624,<br>SRR7429735,<br>SRR7429781,<br>SRR7440567,<br>SRR7440606,<br>SRR7440615,<br>SRR7440618,<br>SRR7440621,<br>SRR7440634,<br>SRR7440649,<br>SRR7440688,<br>SRR7440921,<br>SRR7441075,<br>SRR7441146,<br>SRR7441209,<br>SRR7441250,<br>SRR7441287,<br>SRR7547848,<br>SRR7827106,<br>SRR7828078,<br>SRR7839361,<br>SRR7841130,<br>SRR7841155,<br>SRR7841205,<br>SRR7842337,<br>SRR7850202,<br>SRR7850362,<br>SRR7850428,<br>SRR7850452,<br>SRR7866225,<br>SRR7866376,<br>SRR7866514,<br>SRR7866571,<br>SRR7866588,<br>SRR7866636,<br>SRR7866672,<br>SRR7866727,<br>SRR7866750,<br>SRR7866891,<br>SRR7873595,<br>SRR7873692,<br>SRR7873717,</td><td></td></tr></tbody></table>
<table><thead><tr><th rowspan="2">cgMLST Type<br>(CC, serogroup)</th><th colspan="2">Source (item)</th><th rowspan="2">Studies from other<br>countries</th><th rowspan="2">Source lab</th><th rowspan="2">NCBI/EBI/DDJJ<br>accession no.</th><th rowspan="2">Reference<br>no.</th></tr><tr><th>This study</th><th>Other studies</th></tr></thead><tbody><tr><td></td><td></td><td></td><td></td><td></td><td>SRR7873744,<br>SRR8235628,<br>SRR8239064,<br>SRR8239220,<br>SRR8239239,<br>SRR8655304,<br>SRR8979699,<br>SRR9004322,<br>SRR9010038</td><td></td></tr></tbody></table>

*A, animal; ANSES, Agence Nationale de Sécurité Sanitaire de L'Alimentation, de L'Environnement et du Travail, FR; CC, clonal complex; CDC, US Centers for Disease Control and Prevention; CL, Chile; DE, Germany; DK, Denmark; ECDC, European Centre for Disease Prevention and Control; F, food; FDA, US Food and Drug Administration; FE, farm environment; FR, France; H, human; IP, Institut Paster, FR; KMAHVH, Klinisk Mikrobiologisk Afdeling, DK; LV, Latvia; MX, Mexico; NO, Norway; PE, food production environment; PL, Poland; RKI, Robert Koch Institut, DE; UK, United Kingdom; UKHSA, UK Health Security Agency, UK; US, United States; UWLMO, University of Warmia and Mazury in Olsztyn, PL.

<figure><img src="image_4.png" /><figcaption>**Appendix Figure 1.** Single linkage dendrogram of 92 isolates generated for genome-based characterization of *Listeria monocytogenes*, Costa Rica. Dendrogram based on cgMLST allelic profiles (1,748-locus scheme). Branches are colored according to lineages: L1, red; L2, blue. Branches are labeled according to lineages, sublineages, and clonal complexes. Information on isolates' name, serogroup, source, sample type, cgMLST type, year of isolation, location, and BIGSdb IDs are provided in the columns. Colors in location column correspond to dots on map. Gray bars indicate clusters of isolates</figcaption></figure>
with ≤7 allelic differences out of 1,748 cgMLST loci. presence of selected virulence and resistance genetic traits in each isolate is represented by squared dark blue boxes and empty boxes denote genes with premature stop codons. BIGSdb, Bacterial Isolate Genome Sequence Database (https://bigsdb.pasteur.fr); CC, clonal complex; cgMLST, core-genome multilocus sequence typing; F, food; H, human; ID, identification; L, lineage; LIPI, listeria pathogenicity island; SL, sublineage; ST, sequence type.

<figure><img src="image_5.png" /><figcaption>**Appendix Figure 2.** Minimum spanning tree of 92 *Lysteria monocytogenes* isolates, Costa Rica, 2009–2019. Trees are based on cgMLST allelic profiles (7-locus scheme). A) Lineage I isolates; B) lineage 2 isolates. Publicly available *L. monocytogenes* isolates (n = 351) from neighboring countries in the Caribbean region were also included. Circles represent different profiles and sizes are proportional to the number of isolates within. Branch lengths are proportional to the allelic differences between the profiles which are indicated in the branches. For simplicity, allelic differences of 1 are omitted and represented by thicker branch lines. Clonal complexes with >1 profile are surrounded by gray shading and labeled if detected in this study or if they contain ≥5 isolates. CC, clonal complex; cgMLST, core-genome multilocus sequence typing; ST, sequence type.</figcaption></figure>
<figure><img src="image_6.png" /><figcaption>**Appendix Figure 3.** Minimum spanning tree of 92 *Lysteria monocytogenes* isolates, Costa Rica, 2009–2019. Trees are based on cgMLST allelic profiles (1,748-locus scheme). A) Lineage I isolates; B) lineage 2 isolates. Circles represent different profiles and sizes are proportional to the number of isolates within. Labels next to circles indicate the source of isolates. Branch lengths are proportional in logarithmic scale to allelic differences between profiles, which are also indicated in the branches. For simplicity, allelic differences of ≤7 are omitted and represented by thicker branch lines. Clusters with >1 profile are highlighted in colors; labels correspond with cgMLST type and are delimited by gray shadows. Dashed ellipses delimitate sublineages with >1 isolate and labeled with corresponding sublineage. cgMLST, core-genome multilocus sequence typing; CT, cgMLST type; F, food; H, human, PE; production environment; SL, sublineage.</figcaption></figure>